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Blastocystis is frequently reported in fecal samples from animals and humans worldwide, and a variety of subtypes (STs) have been observed in wild and domestic animals. In Colombia, few studies have focused on the transmission dynamics and epidemiological importance of Blastocystis in animals. In this study, we characterized the frequency and subtypes of Blastocystis in fecal samples of domestic animals including pigs, minipigs, cows, dogs, horses, goats, sheep, and llama from three departments of Colombia. Of the 118 fecal samples included in this study 81.4% ( n = 96) were positive for Blastocystis using a PCR that amplifies a fragment of the small subunit ribosomal RNA ( SSU rRNA) gene. PCR positive samples were sequenced by next generation amplicon sequencing (NGS) to determine subtypes. Eleven subtypes were detected, ten previously reported, ST5 (50.7%), ST10 (47.8%), ST25 (34.3%), ST26 (29.8%), ST21 (22.4%), ST23 (22.4%), ST1 (17.9%), ST14 (16.4%), ST24 (14.9%), ST3 (7.5%), and a novel subtype, named ST32 (3.0%). Mixed infection and/or intra -subtype variations were identified in most of the samples. Novel ST32 was observed in two samples from a goat and a cow. To support novel subtype designation, a MinION based sequencing strategy was used to generate the full-length of the SSU rRNA gene. Comparison of full-length nucleotide sequences with those from current valid subtypes supported the designation of ST32. This is the first study in Colombia using NGS to molecularly characterize subtypes of Blastocystis in farm animals. A great diversity of subtypes was observed in domestic animals including subtypes previously identified in humans. Additionally, subtype overlap between the different hosts examined in this study were observed. These findings highlight the presence of Blastocystis subtypes with zoonotic potential in farm animals indicating that farm animals could play a role in transmission to humans.

The ability to identify compositional changes in the intestinal microbiota of parasitized hosts is important for understanding the physiological processes that may affect animal productivity. Within the field of host–parasite interactions, many studies have suggested that helminths can influence the microbial composition of their hosts via their immunomodulatory effects. Bovine fascioliasis is a helminthiasis widely studied by immunologists, but with little information available regarding gut microbial communities. Thus, we aimed to describe the composition of the intestinal microbiota of Holstein Fasciola -positive and -negative cattle using parasitological methods and ELISA (enzyme-linked immunosorbent assay). Bovine fecal samples (n = 65) were obtained from livestock slaughter plants in the Cundi-Boyacense Colombian highlands (a hyperendemic region for bovine fascioliasis) and studied by amplicon-based next-generation 16S-rRNA and 18S-rRNA gene sequencing. From these samples, 35 were Fasciola hepatica -negative and, 30 were F . hepatica -positive in our detection analysis. Our results showed a reduction in the relative abundance of Bacteroidetes and Ascomycota in the Fasciola -positive samples, along with decreased relative abundances of the commensal taxa previously associated with fermentation and digestion processes. However, metabolomic approaches and functional analyzes of the intestinal microbiota are necessary to support these hypothesis. These findings are a small first step in the development of research aimed at understanding how microbial populations in bovines are modulated in liver helminth infections.

Rhipicephalus sanguineus sensu lato (s.l.), commonly known as the domestic dog tick, is a globally distributed tick. This species plays a significant role in human and animal health, as well as in economy due to its ability to infest livestock. The use of shotgun metagenomics has proven valuable in identifying tick-borne pathogens and key members of the tick microbiome, including endosymbionts. However, the application of shotgun metagenomics in R. sanguineus s.l. ticks in Latin America remains largely unexplored. Therefore, our objective aimed to explore and further analyze the metagenome of the tropical lineage of R. sanguineus s.l. ticks in Colombia. Through our analysis, we identified the three most prevalent pathogens harbored by these ticks, namely: Anaplasma phagocytophilum , Francisella tularensis , and Theileria equi . However, the most abundant microorganism detected was not a pathogen but the endosymbiont Coxiella mudrowiae . Interestingly, Coxiella mudrowiae exhibited significant negative correlations with several pathogens and other endosymbionts. Furthermore, we successfully constructed 27 medium-quality metagenome-assembled genomes (MAGs) for this microorganism, enabling us to conduct a pangenome analysis by comparing them with available genomes and identifying proteins of interest, such as those involved in vitamin B synthesis. This study represents the first implementation of shotgun metagenomics as a methodology to expand our understanding of pathogens and endosymbionts in the circulating tropical lineage of R. sanguineus s.l. ticks in Colombia. The findings of this research serve as a foundation for the development of prevention and mitigation strategies against pathogens transmitted by this tick species. Information gained from this study can contribute to the improvement of public health measures and veterinary practices aimed at controlling the impact of tick-borne diseases.

The productivity of cattle farms is affected by infectious and noninfectious factors that generate economic losses and cause reproductive failure represented by low conception rates, embryonic mortality, abortions, and fetal mummification. The infectious agents that most impact the reproductive health of the bovine species from conception to birth are bovine herpesvirus type 1 (BoHV-1) causing infectious bovine rhinotracheitis (IBR), bovine viral diarrhea virus (BVDV), bovine parainfluenza virus type 3 (PI3), Neospora caninum and Leptospira spp. The objective of this study was to diagnose the presence of BoHV-1, bovine viral diarrhea (BVD), PI3, Neospora caninum, and Leptospira spp. by serology and identify the risk factors associated with infectious agents of reproductive interest in bovines of Boyacá (Colombia). A descriptive cross-sectional study was developed, with simple random sampling, where a sample size of 601 female cattle of Holstein, Jersey, and Normande breeds of different age groups was determined. Blood samples were taken and processed using the indirect ELISA technique (SYNBIOTICS®, SERELISA® BVD p80 Ab Mono Blocking, Ingezim R.12.NC.K, PRIMACHECK VPI-3®) and the MAT test for the diagnosis of bovine leptospirosis. The data were processed with the statistical program Epi Info™. The highest apparent seroprevalence was established for infectious bovine rhinotracheitis (61.1%), followed by BVD (37.6%), PI3 (40.9%), neosporosis (51.1%), and leptospirosis (14.8%). Variables such as age >4 years and Holstein breed for IBR and >4 years for BVD were established risk factors. Considering our results, we suggest implementing prevention and control plans that include vaccination as a prophylactic measure and biosecurity tools that reduce the probability of contagion and transmission of pathogens.

Cattle have a significant impact on human societies in terms of both economics and health. Viral infections pose a relevant problem as they directly or indirectly disrupt the balance within cattle populations. This has negative consequences at the economic level for producers and territories, and also jeopardizes human health through the transmission of zoonotic diseases that can escalate into outbreaks or pandemics. To establish prevention strategies and control measures at various levels (animal, farm, region, or global), it is crucial to identify the viral agents present in animals. Various techniques, including virus isolation, serological tests, and molecular techniques like PCR, are typically employed for this purpose. However, these techniques have two major drawbacks: they are ineffective for non-culturable viruses, and they only detect a small fraction of the viruses present. In contrast, metagenomics offers a promising approach by providing a comprehensive and unbiased analysis for detecting all viruses in a given sample. It has the potential to identify rare or novel infectious agents promptly and establish a baseline of healthy animals. Nevertheless, the routine application of viral metagenomics for epidemiological surveillance and diagnostics faces challenges related to socioeconomic variables, such as resource availability and space dedicated to metagenomics, as well as the lack of standardized protocols and resulting heterogeneity in presenting results. This review aims to provide an overview of the current knowledge and prospects for using viral metagenomics to detect and identify viruses in cattle raised for livestock, while discussing the epidemiological and clinical implications.

Clostridium perfringens inhabits the guts of humans and animal species. C. perfringens can proliferate and express an arsenal of toxins, promoting the development of multiple gut illnesses. Healthy animals carrying C. perfringens represents a risk of transmission to other animals or humans through close contact and an increased likelihood of acquisition of toxin plasmids. The aim of this study was to evaluate the frequency of C. perfringens carriage in domestic and farm animals in the central highlands of Colombia. C. perfringens was detected in six animal species using PCR targeting alpha toxin (cpa) and 16S ribosomal RNA (16S-rRNA) genes from 347 fecal samples collected in two Departments: 177 from farm animals of Boyacá and 170 from domestic animals of both Cundinamarca and Boyacá. The overall frequency of C. perfringens detection was 22.1% (n = 77/347), with the highest frequency observed in cats 34.2% (n = 41/120), followed by dogs 30.0% (n = 15/50). The lowest frequency was detected in ruminants: goats 11.1% (n = 3/27), sheep 8.0% (n = 4/50) and cattle 6.0% (n = 6/50). Domestic animals showed a higher frequency of C. perfringens carriage than farm animals. This difference could be associated with dietary patterns, as domestic animals have diets rich in proteins and carbohydrates, while ruminants have low-carbohydrate diets, resulting in high production of endopeptidase-type enzymes and differences in pH due to the anatomy of gastrointestinal tract, which can influence bacterial proliferation. These findings indicate a potential risk of transmission of C. perfringens among animals and from animals to humans through close contact.

Fasciola hepatica is a zoonotic trematode that affects a wide range of hosts, including cattle, sheep, and goats. The economic impact of the parasite on the cattle industry is significant, with high losses reported worldwide. While its impact on human health was previously underestimated, recent years have seen a rise in fascioliasis cases, leading to increased interest among researchers globally. To characterize the genetic diversity and intraspecific variation of this parasite in South America, specifically in Colombia, we collected 105 adult parasites from cattle bile ducts in seven Colombian departments (Antioquia, Boyacá, Santander, Cauca, Cundinamarca, Nariño, Norte de Santander, and Santander) to assess the parasite’s phenotypic analyses, genetic diversity, and population structure. A computer image analysis system (CIAS) was applied based on standardized morphological measurements. Liver-fluke size was studied by principal component analysis (PCA). DNA sequences were obtained for nuclear markers such as the 28S, β-tubulin 3, ITS1, ITS2, and the mitochondrial marker Cytochrome Oxidase I (COI). Multiple statistical tests were performed, and the parasite’s population structure was analyzed. Maximum Likelihood (ML) phylogenetic reconstructions were carried out using the sequences obtained herein and sequences available in GenBank. Morphological results revealed that all the obtained individuals matched F. hepatica ’s morphology. There was no evidence of high genetic diversity, and the absence of genetic structure at the country-level was notable, possibly caused by a demographic expansion of this trematode in Colombia or the low resolution of the molecular markers employed. Future studies are still needed to unveil the genetic population structure of F. hepatica across the country.

El control de nematodos gastrointestinales en ovinos es realizado casi exclusivamente con productos de origen químico que, por lo general, ofrecen buenos resultados. Sin embargo, su inadecuado uso ha generado la presencia de resistencia en algunos grupos parasitarios. Consecuente con esto, y teniendo en cuenta que cada vez es mayor la preocupación encaminada hacia el consumo de alimentos inocuos que favorezcan la salud humana, se ha buscado desarrollar nuevos métodos de control de origen biológico que permitan manejar y controlar la presencia de parásitos gastrointestinales al interior de las explotaciones pecuarias mediante la utilización de enemigos naturales contra estos agentes patógenos en el medio ambiente. Dentro de los métodos biológicos más utilizados para el control de nematodos gastrointestinales en ovinos se encuentran los hongos nematófagos, los cuales tienen propiedades como la reducción del número de larvas de nematodos en materia fecal y la facilidad de atravesar el tracto gastrointestinal preservando su capacidad germinativa, lo que facilita la posibilidad de desarrollar variadas formas de administración. En la presente revisión se tratarán las especies de hongos nematófagos más utilizadas, así como las distintas formas de administración ensayadas en la actualidad.

The control of gastrointestinal nematodes in sheep is almost exclusively done with chemical products that generally offer good results, however inappropriate use has generated the presence of resistance in some parasitic groups. Consistent with this, and taking into account that there is a growing concern directed towards the consumption of safe food that favour human health, has sought develop new methods of biological control that manage and control the presence of gastrointestinal parasites inside of livestock farms through the use of natural enemies against these pathogens in the environment. The nematopahgous fungi, which have properties such as the reduction of the number of larvae of nematodes in fecal matter and ease of passing through the gastrointestinal tract while preserving its germinative capacity, which facilitates the possibility of developing various forms of administration are among the more biological methods for the control of gastrointestinal nematodes in sheep. In the present review were the species of fungi nematophagous most commonly used, as well as the different forms of administration tested today.