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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. [ABSTRACT FROM AUTHOR]

The global presence of SARS-CoV-2 in household pets is acknowledged, yet documentation remains scarce, leaving many regions unexplored. Thus, our study sought to fill this gap by investigating SARS-CoV-2 presence in dogs visiting veterinary clinics during the third pandemic peak in eastern Colombia. We collected and analyzed 43 oropharyngeal and rectal swabs using real-time PCR assays targeting the Envelope Gene of SARS-CoV-2. Out of these, two dogs tested positive, indicating an infection rate of 4.7%. Further examination through complete sequencing and phylogenetic analysis revealed the lineage B.1.621 for the SARS-CoV-2 genome. Consequently, our study unveils the first documented cases of Canis lupus familiaris infected with the Mu variant of SARS‐CoV‐2, the variant with the most death burden during the whole pandemic in Colombia. Remarkably, these cases presented mild and reversible respiratory and gastrointestinal symptoms, or no clinical manifestations at all. This sheds light on the virus's interaction with our four-legged companions, offering valuable insights into its transmission dynamics and potential effects on animal health. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

This study investigated the impact of struvite as a sustainable phosphorus source on the growth and phycocyanin production by the blue-green alga Arthrospira platensis. Three modified growth media were compared to the typical SAG-spirul culture media. CS(+) refers to the completely recycled struvite from bovine urine as a phosphate source, while S(-) and S(+) refer to commercially available struvite as a phosphate source. On media with (+), a pre-treatment was conducted to evaporate NH4, as it negatively affects cell growth and functions of the photosynthetic apparatus at high concentrations, and to release phosphate due to the low solubility of struvite in water. For each medium, three cultures were cultivated in Erlenmeyer flasks for a duration of 42 days. Results showed that no statistically significant negative effect of struvite was found on the growth rates. However, C-phycocyanin (CPC-P) in CS(+) and S(+) was significantly higher compared to CPC-P in untreated growth media. The study hypothesized that low concentrations of NH3 remaining after the pre-treatment of struvite could have a positive impact on phycocyanin accumulation, as an energy efficient and quick nitrogen source for A. platensis. [ABSTRACT FROM AUTHOR]

Wetlands represent key ecosystems due to their remarkable biodiversity, ecological functions and multiple ecosystem services provided. In Colombia, there are 31,702 wetlands, 13 of which are in Bogotá, capital of the country. Despite the fundamental socioecological support of these aquatic ecosystems, a tremendous loss and degradation of these ecosystems has been observed due to anthropogenic perturbations. Therefore, the aim of this study was to describe the status of seven Bogotá wetlands with variable anthropogenic interventions by measuring organoleptic, physicochemical, and microbiological parameters, using commercial kits, highly sensitive equipment, and next-generation sequencing of the 16S- and 18S-rRNA genes. Our findings describe the status of seven wetlands with different anthropogenic burden in Bogotá-Colombia where physicochemical and microbiology signals of contamination were observed. Additionally, some profiles in the composition of the microbial communities, together with certain physicochemical characteristics, may represent an insight into the environmental dynamics, where Beta Proteobacteria such as Malikia represent a potential keystone in aquatic ecosystems impacted by wastewater effluent discharges; the presence of nitrates and phosphates explain the abundance of bacteria capable of oxidizing these compounds, such as Polynucleobacter. Moreover, the presence of specific prokaryotic and eukaryotic organisms, such as Clostridium, Cryptococcus, Candida, and Naegleria, reported in one or more of the wetlands assessed here, could represent a possible pathogenic risk for human and animal health. This study performed a complete evaluation of seven Bogotá wetlands with different anthropogenic impacts for the first time, and our findings emphasize the importance of maintaining continuous monitoring of these water bodies given their remarkable ecological importance and potential spill-over of several pathogens to humans and animals. [ABSTRACT FROM AUTHOR]

Dirofilariasis is a mosquito-borne disease caused by Dirofilaria parasites, affecting both wild and domestic animals, including humans considered as accidental hosts. Dirofilaria repens is the principal causative agent of dirofilariasis in the Old World, with increasing reports of the parasite in countries where it has not been previously identified, due to several factors such as the expansion of mosquito vectors' geographical distribution. By utilizing newly designed primers for molecular detection and confirming through next-generation sequencing, here, we report the first plausible cases of D. repens in dogs from Colombia. Our results support the classification of this species as an emergent pathogen in the Americas. Finally, we encourage an increase in diagnostic and surveillance efforts to prevent and control the current and future dirofilariasis cases in this region. [ABSTRACT FROM AUTHOR]

Chagas disease caused by Trypanosoma cruzi is a public health issue in Latin America. This highly diverse parasite is divided into at least seven discrete typing units (DTUs) TcI-TcVI and Tcbat. Some DTUs have been associated with geographical distribution in epidemiological scenarios and clinical manifestations, but these aspects remain poorly understood. Many studies have focused on studying the parasite and its vectors/hosts, using a wide variety of genetic markers and methods. Here, we performed a systematic review of the literature for the last 20 years to present an update of DTUs distribution in the Americas, collecting ecoepidemiological information. We found that the DTUs are widespread across the continent and that there is a whole gamma of genetic markers used for the identification and genotyping of the parasite. The data obtained in this descriptor could improve the molecular epidemiology studies of Chagas disease in endemic regions. Measurement(s) Genotype Technology Type(s) Report from Literature [ABSTRACT FROM AUTHOR]

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of the current COVID-19 pandemic, has evolved to have a wide range of hosts, including non-human primates, wild and domestic animals. The ACE2 protein has a high level of conservation and is the common receptor invertebrate species for a viral infection to occur; this receptor could give rise to anthroponotic events. This article describes the first event of symptomatic transmission in Latin America from a human to a dog by the B.1.625 lineage of SARS-CoV-2. We found 21 shared mutations in the complete genomes of viral sequences from owners and dogs. Further phylogenetic and molecular analysis showed that 100% co-localization of the clade helps to understand human-animal transmission. Prediction of the Spike protein structure of the sequenced virus and docking analyzes showed that the E484K mutation in the receptor-binding domain (RBD) could contribute to the viral affinity of dACE2. Therefore, close contact between SARS-CoV-2-infected humans and pets should be avoided to prevent the emergence of novel mutations of public health importance from anthroponotic events. [ABSTRACT FROM AUTHOR]

The role of gut microbiota in the establishment and development of Clostridioides difficile infection (CDI) has been widely discussed. Studies showed the impact of CDI on bacterial communities and the importance of some genera and species in recovering from and preventing infection. However, most studies have overlooked important components of the intestinal ecosystem, such as eukaryotes and archaea. We investigated the bacterial, archaea, and eukaryotic intestinal microbiota of patients with health-care-facility- or community-onset (HCFO and CO, respectively) diarrhea who were positive or negative for CDI. The CDI-positive groups (CO/+, HCFO/+) showed an increase in microorganisms belonging to Bacteroidetes, Firmicutes, Proteobacteria, Ascomycota, and Opalinata compared with the CDI-negative groups (CO/−, HCFO/−). Patients with intrahospital-acquired diarrhea (HCFO/+, HCFO/−) showed a marked decrease in bacteria beneficial to the intestine, and there was evidence of increased Archaea and Candida and Malassezia species compared with the CO groups (CO/+, CO/−). Characteristic microbiota biomarkers were established for each group. Finally, correlations between bacteria and eukaryotes indicated interactions among the different kingdoms making up the intestinal ecosystem. We showed the impact of CDI on microbiota and how it varies with where the infection is acquired, being intrahospital-acquired diarrhea one of the most influential factors in the modulation of bacterial, archaea, and eukaryotic populations. We also highlight interactions between the different kingdoms of the intestinal ecosystem, which need to be evaluated to improve our understanding of CDI pathophysiology. [ABSTRACT FROM AUTHOR]

Microbial communities in surface waters used for recreational purposes are indicators of contamination and risk of contact with human pathogens. Hence, monitoring microbial communities in recreational waters is important for potential public health threats to humans. Such monitoring is rare in Colombia, even in its capital, Bogotá, the most populous city in the country. This city encompasses metropolitan and linear parks with recreational water bodies that are used frequently by the public, and the presence of pathogens can compromise the health of the citizens. Therefore, we examined the bacterial, and eukaryotic communities in urban recreational lakes (URL) in four metropolitan parks in Bogotá, Colombia. Samples from four metropolitan parks (Los Novios, Simon Bolivar, El Tunal, and Timiza) and one stream contaminated with sewage from a linear park (El Virrey) were collected. We used amplicon next-generation sequencing of the 16S-rRNA gene and 18S-rRNA gene to characterize microbial communities followed by bioinformatics analyses. In addition, general water quality parameters—pH, hardness, acidity, alkalinity, dissolved oxygen, and nitrites—were recorded using a commercial kit. Genera of pathogens, including Legionella, Pseudomonas, Mycobacterium, Candida, and Naegleria, were found in lake waters. The stream El Virrey was, however, the only surface water that showed an abundance of fecal bacteria, often associated with low oxygen concentrations. All water bodies showed a predominance of fungal phyla, except for the lake at Timiza. This lake showed the highest pH, and its ecological dynamics are likely different from other water bodies. Likewise, some URLs displayed a greater abundance of cyanobacteria, including toxin-producing species. Algal genera associated with eutrophication were predominant among primary producing microorganisms. This study shows for the first time the description of the bacterial and eukaryotic communities of some URLs and a stream in Bogotá. The URLs and the stream harbored various pathogens that might pose a risk to the citizen's health. [ABSTRACT FROM AUTHOR]

Desertion of offspring before its independence by one of the parents is observed in a number of avian species with bi-parental care but reasons for this strategy are not fully understood. This behaviour is particularly intriguing in species where bi-parental care is crucial to raise the brood successfully. Here, we focus on the little auk, Alle alle, a small seabird with intensive bi-parental care, where the female deserts the brood at the end of the chick rearing period. The little auk example is interesting as most hypotheses to explain desertion of the brood by females (e.g. "re-mating hypothesis", "body condition hypothesis") have been rejected for this species. Here, we analysed a possible relationship between the duration of female parental care over the chick and her chances to survive to the next breeding season. We performed the study in two breeding colonies on Spitsbergen with different foraging conditions – more favourable in Hornsund and less favourable in Magdalenefjorden. We predicted that in Hornsund females would stay for shorter periods of time with the brood and would have higher survival rates in comparison with birds from Magdalenefjorden. We found that indeed in less favourable conditions of Magdalenefjorden, females stay longer with the brood than in the more favourable conditions of Hornsund. Moreover, female survival was negatively affected by the length of stay in the brood. Nevertheless, duration of female parental care over the chick was not related to their parental efforts, earlier in the chick rearing period, and survival of males and females was similar. Thus, although females brood desertion and winter survival are linked, the relationship is not straightforward. Significance statement: When bi-parental care is crucial to raise the brood successfully, one parent desertion raises the question of why this happens. We examined this issue in the little auk, a small seabird with females deserting the brood at the end of the chick rearing period. We hypothesised that females deserting the brood save residual energy and, in this way, increases their chance to survive to the next breeding season. We found that duration of female parental care depends on environmental conditions, with longer staying with the brood in less favourable conditions. As expected, female survival decreased with duration of their staying with the brood but it was not related to their parental efforts (i.e. number of chick feedings, duration of foraging flights). In addition, survival of males and females was similar. Thus, although little auk females brood desertion and winter survival are linked, the relationship is not straightforward. [ABSTRACT FROM AUTHOR]

This study describes a rapid method for sequential determination of uranium and plutonium isotopes in soil and sediment samples and its application to the study of Anthropocene sedimentary records. Different pretreatment methods have been tested (open-vessel digestion, borate salts fusion and NaOH salt fusion) achieving the complete dissolution of the sample in case of fusion methods. LiBO2 and Li2B4O7 (80/20) flux was finally selected because a higher amount of sample can be analyzed (up to 5 g). Moreover, separation steps with extraction chromatographic resin UTEVA were optimized. Average recoveries obtained for uranium and plutonium were acceptable, 59% and 72% respectively, and relative bias were below ± 15%. The time to complete the separation is approximately 11 h without ashing the samples and, consequently, it can be used in emergencies. [ABSTRACT FROM AUTHOR]

This study describes a rapid and novelty method for radiostrontium determination in aerosol filters and vegetation based on the use of plastic scintillation resins (PS resin), which combines the separation and measurement preparation into a single step. The optimization of the pre-treatment steps and the use of PS resin allows a simplification of the radiochemistry and a reduction in the time of analysis to 8 h and 12 h for aerosol filters and vegetation, respectively. The limits of detection were on average 0.04 Bq (filter)−1 and 3 Bq (kg-fresh)−1. The method obtained high recoveries (82% on average) and relative bias for total radiostrontium were below 30%. Individual activities of 89Sr and 90Sr were obtained by deconvolution methods. [ABSTRACT FROM AUTHOR]

This study describes a new and rapid procedure for radiostrontium determination in milk samples based on the use of plastic scintillation resins (PS resins). The proposed method reduces the time of analysis by at least 2 h by combining separation and measurement preparation into a single step and optimizing the pre-treatment steps. The method is robust and reproducible, with good total recoveries (65% on average) and a relative bias for total radiostrontium activity (89Sr + 90Sr) below 7%. The minimum detectable activity for 100 mL of milk sample measured for 60 min is about 0.34 Bq L-1. The proposed method can quantify radiostrontium content in 5 h, which makes it suitable for use in emergency situations. [ABSTRACT FROM AUTHOR]

Introduction: Liver-kidney transplantation is a rare procedure in children, with just ten to 30 cases performed annually worldwide. The main indications are autosomal recessive polycystic liver-kidney disease and primary hyperoxaluria. This study aimed to report outcomes of liver-kidney transplantation in a cohort of pediatric patients. Methods: We retrospectively analyzed all pediatric liver-kidney transplantations performed in our center between September 2000 and August 2015. Patient data were obtained by reviewing inpatient and outpatient medical records and our transplant database. Results: A total of 14 liver-kidney transplants were performed during the study period, with a median patient age and weight at transplant of 144.4 months (131.0-147.7) and 27.3 kg (12.0-45.1), respectively. The indications for liver-kidney transplants were autosomal recessive polycystic liver-kidney disease (8/14), primary hyperoxaluria −1 (5/14), and idiopathic portal hypertension with end-stage renal disease (1/14). Median time on waiting list was 8.5 months (5.7-17.3). All but two liver-kidney transplants were performed simultaneously. Patients with primary hyperoxaluria-1 tended to present a delayed recovery of renal function compared with patients transplanted for other indications (62.5 vs 6.5 days, respectively, P 0.076). Patients with liver-kidney transplants tended to present a lower risk of acute kidney rejection than patients transplanted with an isolated kidney transplant (7.2% vs 32.7%, respectively; P < 0.07). Patient and graft survival at 1, 3, and 5 years were 100%, 91.7%, 91.7%, and 91.7%, 83.3%, 83.3%, respectively. No other grafts were lost. Conclusion: Long-term results of liver-kidney transplants in children are encouraging, being comparable with those obtained in isolated liver transplantation. [ABSTRACT FROM AUTHOR]

DNA cloning is an essential tool regarding DNA recombinant technology as it allows the replication of foreign DNA fragments within a cell. pELMO was here constructed as an in-house cloning vector for rapid and low-cost PCR product propagation; it is an optimally designed vector containing the ccdB killer gene from the pDONR 221 plasmid, cloned into the pUC18 vector's multiple cloning site (Thermo Scientific). The ccdB killer gene has a cleavage site (CCC/GGG) for the SmaI restriction enzyme which is used for vector linearisation and cloning blunt-ended products. pELMO transformation efficiency was evaluated with different sized inserts and its cloning efficiency was compared to that of the pGEM-T Easy commercial vector. The highest pELMO transformation efficiency was observed for ~500 bp DNA fragments; pELMO vector had higher cloning efficiency for all insert sizes tested. In-house and commercial vector cloned insert reads after sequencing were similar thus highlighting that sequencing primers were designed and localised appropriately. pELMO is thus proposed as a practical alternative for in-house cloning of PCR products in molecular biology laboratories. [ABSTRACT FROM AUTHOR]

Background: There are no guidelines for the removal of a failed renal allograft, and its impact on subsequent dialysis and retransplantation has not yet been described. Methods: We performed a 10-year review of allograft failure to study the factors that determined an outcome of transplant nephrectomy and choice of subsequent renal replacement therapy in children with or without nephrectomy. Results: A total of 34 children developed graft failure over the 10-year study period, of whom 18 (53 %) required transplant nephrectomy. The median graft survival was 1.1 (range 0.2-10.6) versus 7.5 (1.5-15.0) years in the nephrectomy and non-nephrectomy groups, respectively ( p = 0.011). Children with graft failure within 1 year of transplantation were four-fold more likely to require transplant nephrectomy than those with graft failure after 1 year ( p = 0.04). Renal biopsy performed at ≤8 weeks prior to graft loss showed Banff grade II acute rejection in 13 of the 18 children who required subsequent nephrectomy versus three of the 13 children who did not need nephrectomy ( p = 0.01). Inflammation (fever, graft tenderness and raised C-reactive protein (CRP) in the 2 weeks preceding graft failure) was seen in 66 % of nephrectomized children, but not in any in the non-nephrectomy group ( p = 0.0003 for CRP between groups). Banff II rejection, an inflammatory response and the time post-transplantation significantly and independently predicted the outcome of nephrectomy ( p = 0.008, R = 67 %). Human leukocyte antigen (HLA) antibody levels after graft failure were higher in the nephrectomy group ( p = 0.0003), but there was no difference between groups in terms of the presence or class of donor-specific antibodies. Of the children with graft failure, 82 % required dialysis (61 % hemodialysis) and 35 % have to date been successfully retransplanted. Conclusions: Children with Banff II rejection, an inflammatory response and early graft loss are more likely to require transplant nephrectomy. Nephrectomy may be associated with higher circulating HLA antibody levels. [ABSTRACT FROM AUTHOR]

Background: Atypical hemolytic uremic syndrome (aHUS) is a rare genetic disorder caused by chronic uncontrolled complement activation. Case-diagnosis/treatment: We present a 4-year-old girl with aHUS who had multiple severe clinical manifestations of thrombotic microangiopathy (TMA) including acute kidney injury, dilated cardiomyopathy, and cardiorespiratory arrest. She was managed with intensive plasma exchange and hemodialysis, which could not halt the progression of TMA. The initial single dose of eculizumab only temporarily improved the clinical symptoms of TMA. Sustained improvement of renal, hematological, and cardiac values were only achieved upon institution of chronic treatment with eculizumab. During long-term treatment with eculizumab (>2.5 years), she has had no further clinical manifestations of TMA, and required neither plasma exchange nor hemodialysis. Conclusion: Chronic eculizumab treatment was associated with control of complement-mediated TMA and sustained long-term improvement in renal and cardiac function. [ABSTRACT FROM AUTHOR]

Clostridium difficile, the causal agent of antibiotic-associated diarrhea, has a complex epidemiology poorly studied in Latin America. We performed a robust genomic and phenotypic profiling of 53 C. difficile clinical isolates established from diarrheal samples from either intrahospital (IH) or community (CO) populations in central Colombia. In vitro tests were conducted to evaluate the cytopathic effect, the minimum inhibitory concentration of ten antimicrobial agents, the sporulation efficiency and the colony forming ability. Eleven different sequence types (STs) were found, the majority present individually in each sample, however in three samples two different STs were isolated. Interestingly, CO patients were infected with STs associated with hypervirulent strains (ST-1 in Clade-2). Three coexistence events (two STs simultaneously detected in the same sample) were observed always involving ST-8 from Clade-1. A total of 2,502 genes were present in 99% of the isolates with 95% of identity or more, it represents a core genome of 28.6% of the 8,735 total genes identified in the set of genomes. A high cytopathic effect was observed for the isolates positive for the two main toxins but negative for binary toxin (TcdA+/TcdB+/CDT− toxin production type), found only in Clade-1. Molecular markers conferring resistance to fluoroquinolones (cdeA and gyrA) and to sulfonamides (folP) were the most frequent in the analyzed genomes. In addition, 15 other markers were found mostly in Clade-2 isolates. These results highlight the regional differences that C. difficile isolates display, being in this case the CO isolates the ones having a greater number of accessory genes and virulence-associated factors. [ABSTRACT FROM AUTHOR]