SARS-CoV-2 infection in brown-headed spider monkeys (Ateles fusciceps) at a wildlife rescue center on the coast of Ecuador-South America.

Human populations can be affected in unpredictable ways by the emergence and spread of zoonotic diseases. The COVID-19 (coronavirus disease of 2019) pandemic was a reminder of how devastating these events can be if left unchecked. However, once they have spread globally, the impact of these diseases when entering non-exposed wildlife populations is unknown. The current study reports the infection of brown-headed spider monkeys (Ateles fusciceps) at a wildlife rescue center in Ecuador. Four monkeys were hospitalized, and all tested positive for SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) by RT-qPCR (Quantitative Reverse Transcription PCR). Fecal samples (n = 12) from monkeys at the rescue center also tested positive; three zookeepers responsible for feeding and deworming the monkeys also tested positive, suggesting human-animal transmission. Whole genome sequencing identified most samples' omicron clade 22B BA.5 lineage. These findings highlight the threat posed by an emerging zoonotic disease in wildlife species and the importance of preventing spillover and spillback events during epidemic or pandemic events.IMPORTANCEAlthough COVID-19 (coronavirus disease of 2019) has been primarily contained in humans through widespread vaccination, the impact and incidence of SARS-CoV-2 (Severe acute respiratory syndrome coronavirus) and its transmission and epidemiology in wildlife may need to be addressed. In some natural environments, the proximity of animals to humans is difficult to control, creating perfect scenarios where susceptible wildlife can acquire the virus from humans. In these places, it is essential to understand how transmission can occur and to develop protocols to prevent infection. This study reports the infection of brown-headed spider monkeys with SARS-CoV-2, a red-listed monkey species, at a wildlife recovery center in Ecuador. This study reports the infection of brown-headed spider monkeys with SARS-CoV-2, indicating the potential for transmission between humans and wildlife primates and the importance of preventing such events in the future.

Delayed acquisition of airway commensals in antibiotic naïve children and its relationship with wheezing in rural Ecuador.

Introduction: The hygiene hypothesis identified a relationship between living in rural areas and acquiring protective environmental factors against the development of asthma and atopy. In our previous study, we found a correlation between particular bacterial species and early-onset wheezing in infants from the rural tropics of Ecuador who were corticosteroid-naïve and had limited antibiotic exposure. We now describe a longitudinal study of infants conducted to determine the age-related changes of the microbiome and its relationship with wheezing. Methods: We performed an amplicon sequencing of the 16S rRNA bacterial gene from the oropharyngeal samples obtained from 110 infants who had a history of recurrent episodic wheezing sampled at different ages (7, 12, and 24 months) and compared it to the sequencing of the oropharyngeal samples from 150 healthy infants sampled at the same time points. Bioinformatic analyses were conducted using QIIME and R. Results: As expected, the microbiota diversity consistently increased as the infants grew older. Considering age-based microbiota changes, we found that infants with wheeze had significantly lower species richness than the healthy infants at 7 months, but not at 12 or 24 months. Most of the core and accessory organisms increased in abundance and prevalence with age, except for a few which decreased. At 7 months of age, infants with wheeze had notably higher levels of a single Streptococcus operational taxonomic unit and core microbiota member than controls. Conclusions: In a cohort with limited antibiotic and corticosteroid use, a progressively more complex and diverse respiratory microbial community develops with age. The respiratory microbiota in early life is altered in infants with wheeze, but this does not hold true in older infants.

Evaluation of changes in the faecal resistome associated with children's exposure to domestic animals and food animal production.

OBJECTIVES: The paediatric gut microbiota is a reservoir of antimicrobial resistance genes. Environmental factors such as a child's exposure to faecal contamination and antimicrobial resistance genes of animal origin likely shape the resistome of infants and children. This study measured how different levels of exposure to domestic or food animals affect the structure of the intestinal resistome in children between 1 and 7 years of age. METHODS: One hundred nineteen faecal samples from 39 children were analysed according to the level of exposure to domestic or food animals and categorized into three risk groups. Using high-throughput sequencing with an Illumina NovaSeq 6000 SP platform, we performed faecal resistome analyses using the ResFinder database. Additionally, ResistoXplorer was used to characterize the resistomes of children differentially exposed to domestic animals. RESULTS: Our data indicated that specific antimicrobial resistance genes such as those that confer resistance to MATFPR (macrolide, aminoglycoside, tetracycline, fluoroquinolone, phenicol, and rifamycin) and tetracyclines were statistically less abundant in the group of children without exposure to animals (group 2), compared with the groups exposed to domestic and food animals (groups 1 and 3). However, the overall resistome structure among the children was not affected by the different levels of exposure to animals. CONCLUSIONS: This study suggests that animal exposure is a risk factor for young children acquiring specific antimicrobial resistance genes from domestic animals or animal production areas. However, the overall resistome structure was not affected.

A longitudinal study of dominant E. coli lineages and antimicrobial resistance in the gut of children living in an upper middle-income country.

OBJECTIVES: The gastrointestinal tract constitutes a complex and diverse ecosystem. Escherichia coli is one of the most frequently studied and characterised species in the gut ecosystem; nevertheless, there has been little research to determine their diversity and population dynamics in the intestines of children over time. We analysed the turnover or dominant E. coli isolates in children faecal matter during 1 year. METHODS: In this prospective study, a fresh faecal sample was obtained from children longitudinally over one year (30 faecal samples at sampling period 1 and 22 faecal samples at sampling periods 2 and 3). From each stool sample, five E. coli colonies were randomly selected (n = 405 E. coli isolates total) in order to characterize the genotype and phenotypic antimicrobial resistance patterns. RESULTS: We were unable to find same E. coli dominant clone in faecal matter from 30 children in different sampling periods. Whole-genome sequencing of three isolates belonging to ST131 found in one child during the sampling period I and II indicated that isolates were three different ST 131 clones that carried extended-spectrum ß-lactamase (ESBL) genes. CONCLUSION: We found that all numerically dominant E. coli lineages in children's intestines were transient colonisers, and antimicrobial resistance phenotypes of these strains varied significantly over time without any apparent selective force.

Duodenal microbiome in patients with or without Helicobacter pylori infection.

BACKGROUND: Intestinal microbiota are recognized as an organ with important physiological functions whose alterations have been associated with common diseases including inflammatory intestinal conditions, malnutrition, type-2 diabetes, and cardiovascular diseases. The composition and function of the microbiota in the distal part of the intestine has been mainly described, while there is limited information on the small intestine microbiota. The objective of the present study was to describe the duodenal microbiome in individuals with dyspepsia in the presence or absence of Helicobacter pylori gastric infection. MATERIALS AND METHODS: Thirty-eight biopsies from the proximal duodenum of uninfected and 37 from H pylori-infected individuals were analyzed. Microbiota composition was assessed by PCR amplification and sequencing of 16S rRNA and ITS genes; sequences were analyzed with QIIME2. RESULTS AND CONCLUSIONS: At the phyla level, Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Fusobacteria were predominant in the mucosal associated duodenal microbiota (MAM); at the genera level, we observed the predominance of Ralstonia, Streptococcus, Pseudomonas, Haemophilus, Herbaspirillum, Neisseria, and Veillonella. Microbiota α-diversity was higher in H pylori-infected individuals than in non-infected ones. In terms of ß-diversity metrics, there was a statistically significant difference between groups. Also, relative abundance of Haemophilus, Neisseria, Prevotella pallens, Prevotella 7, and Streptococcus was greater in H pylori-infected patients. In infected patients, several types of H pylori were present in duodenal MAM. Finally, the majority of duodenal samples had fungi sequences; the most common taxa observed were Recurvomyces followed by Ascomycota and Basidiomycota.

Effect of Saccharomyces boulardii CNCM I-745 as complementary treatment of Helicobacter pylori infection on gut microbiome.

Conventional therapy for H. pylori infection includes the combination of antibiotics and a proton-pump inhibitor. Addition of probiotics as adjuvants for H. pylori antibiotic treatment can increase eradication rate and decrease treatment side effects. Although many studies show the benefits of S. boulardii CNCM I-745 in the treatment of H. pylori infection, the mechanism by which those benefits are achieved is unknown. Here, we report clinical characteristics and fecal microbiota changes comparing conventional anti-H. pylori therapy versus conventional therapy supplemented with S. boulardii CNCM I-745. A total of 74 patients were included in the current study; patients positive for H. pylori (n = 63) were randomly assigned to 2 groups: 34 patients received conventional therapy and 29 antibiotic therapy plus 750 mg of S. boulardii CNCM I-745 daily, for 2 weeks. Eleven patients negative for H. pylori infection were also studied. Patients provided 3 fecal samples: before initiating the antibiotic treatment, upon its completion, and 1 month after treatment. Patients were contacted every 72 h to inquire about side effects and compliance. DNA was extracted, and 16S rRNA was amplified and sequenced on Illumina MiSeq. Bioinformatic analysis was performed using QIIME2. Patients who received the probiotic had a significantly lower frequency of associated gastrointestinal symptoms (P = 0.028); higher number of bacterial diversity evenness (P = 0.0156); higher abundance of Enterobacteria; and lower abundance of Bacteroides and Clostridia upon treatment completion. Addition of S. boulardii CNCM I-745 induced a lower frequency of gastrointestinal symptoms that could be related to changes in gut microbiota.

Analysis of gut microbiome, nutrition and immune status in autism spectrum disorder: a case-control study in Ecuador.

Most studies on autism spectrum disorder (ASD) risk factors have been conducted in developed countries where ethnicity and environment are different than in developing countries. We compared nutritional status, immune response and microbiota composition in mestizo children with ASD with matched controls in Ecuador. Twenty-five cases and 35 controls were matched by age, sex and school location. The prevalence of under- and overweight was higher in children with ASD. Nutritional differences were accompanied by abnormal food habits and more frequent gastrointestinal symptoms in children with ASD. Also, greater serum concentrations of TGF-ß1 were observed in children with ASD. Finally, there was greater alpha diversity and abundance of Bacteroides (2 OTUs), Akkermansia, Coprococcus and different species of Ruminococcus in ASD children.

Molecular typing of a large nosocomial outbreak of KPC-producing bacteria in the biggest tertiary-care hospital of Quito, Ecuador.

OBJECTIVES: Klebsiella pneumoniae is an opportunistic pathogen associated with nosocomial infections worldwide. Isolates with a K. pneumoniae carbapenemase (KPC)-producing phenotype show reduced susceptibility to first-choice antibiotics. Between 2012-2013, the largest public tertiary-care hospital in Quito (Ecuador) reported an outbreak of KPC-producing bacteria with more than 800 cases. We developed a molecular epidemiological approach to analyse the clonality of K. pneumoniae isolates recovered from selected hospital services and patient samples. METHODS: A retrospective cohort study was performed based on microbial isolates and their corresponding records from the hospital and referred to Instituto Nacional de Investigación en Salud Pública (INSPI). From 800 isolates that were collected between 2012-2013, a total of 100 isolates were randomly selected for this study. Antimicrobial susceptibility testing was performed according to Clinical and Laboratory Standards Institute (CLSI) guidelines. Genotypic detection and phylogenetic relationship analysis were performed by multilocus sequence typing (MLST). The blaKPC carbapenemase gene was also amplified by PCR and was sequenced using Sanger sequencing. RESULTS: Molecular analysis showed that the outbreak had a polyclonal origin with two predominant genotypes, comprising sequence types ST25 and ST258, present in 38 and 36 cases, respectively. These genotypes were found in all studied hospital services including general surgery, intensive care unit and emergency. TheblaKPC-5 gene was the most prevalent blaKPC variant in this study. CONCLUSION: These data indicate that KPC-producing polyclonal K. pneumoniae are frequent causes of nosocomial hospital outbreaks in South America. Similar genotypes have been reported in Colombia, Argentina, Brazil, North America and Asia.

Diagnostic Efficacy of Molecular Techniques for Detection and Identification of Leishmania Species in Human Whole Blood and Skin Samples from Ecuador.

Microscopic examination is the standard method for diagnosis of cutaneous and mucocutaneous leishmaniasis despite its low sensitivity. This study compared the diagnosis efficacy of microscopic examination versus polymerase chain reaction (PCR)-based methods and DNA sequencing using whole blood and skin lesion samples from patients with suspected leishmaniasis. The presence of Leishmania was determined by microscopy and amplification of 18S ribosomal RNA gene from blood and skin samples of 22 patients. Twenty individuals were positive for leishmaniasis. Microscopic analysis identified 85%, whereas PCR identified 100% of positive cases from skin and 90% from blood. Cytochrome b gene (cyt-b) amplification and sequencing identified Leishmania guyanensis, Leishmania shawi, and Leishmania naiffi from skin and blood samples. This study demonstrated the usefulness of whole blood and molecular techniques for the diagnosis and species identification of leishmaniasis.

Airway Microbiota in Severe Asthma and Relationship to Asthma Severity and Phenotypes.

BACKGROUND: The lower airways harbor a community of bacterial species which is altered in asthma. OBJECTIVES: We examined whether the lower airway microbiota were related to measures of asthma severity. METHODS: We prospectively recruited 26 severe asthma, 18 non-severe asthma and 12 healthy subjects. DNA was extracted from induced sputum and PCR amplification of the V3-V5 region of bacterial 16S rRNA gene was performed. RESULTS: We obtained 138,218 high quality sequences which were rarefied at 133 sequences/sample. Twenty OTUs had sequences ≥1% of total. There were marked differences in the distribution of Phyla between groups (P = 2.8x10-118). Bacteroidetes and Fusobacteria were reduced in non-severe and severe asthmatic groups. Proteobacteria were more common in non-severe asthmatics compared to controls (OR = 2.26; 95% CI = 1.94-2.64) and Firmicutes were increased in severe asthmatics compared to controls (OR = 2.15; 95%CI = 1.89-2.45). Streptococcal OTUs amongst the Firmicutes were associated with recent onset asthma, rhinosinusitis and sputum eosinophilia. CONCLUSIONS: Sputum microbiota in severe asthma differs from healthy controls and non-severe asthmatics, and is characterized by the presence of Streptococcus spp with eosinophilia. Whether these organisms are causative for the pathophysiology of asthma remains to be determined.

Staphylococcus aureus outbreak in the intensive care unit of the largest public hospital in Quito, Ecuador

Staphylococcus aureus is a frequent cause of nosocomial pneumonia and bacteremia worldwide. Classical and molecular epidemiology approaches were used to study a S. aureus outbreak in the intensive care unit (ICU) of one of the largest public hospitals in Quito. Staphylococcus aureus isolates from 17 patients and 19 potential carriers from the staff were collected from March 2007 to February 2008 and analyzed by pulsed-field gel electrophoresis (PFGE) to determine their clonal relationships. During this period the hospital reported 16 cases of hospital-acquired staphylococcal pneumonia and an apparent outbreak occurred from June to September 2007. DNA from these isolates formed six different PFGE patterns: four clonal groups, and two groups of clonally related isolates. Molecular typing failed to identify any staphylococcal reservoir among staff members. The current study suggested that a staphylococcal outbreak that occurred in the summer of 2007 was caused by different bacterial clones, although some clones were shared by two patients. Historical analysis of the staphylococcal infections in the ICU showed a higher incidence during the summer months, which coincided with the programmed personnel shift. This observation suggests that outbreaks might be produced by the introduction of improperly trained personnel (AU)

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Staphylococcus aureus outbreak in the intensive care unit of the largest public hospital in Quito, Ecuador.

Staphylococcus aureus is a frequent cause of nosocomial pneumonia and bacteremia worldwide. Classical and molecular epidemiology approaches were used to study a S. aureus outbreak in the intensive care unit (ICU) of one of the largest public hospitals in Quito. Staphylococcus aureus isolates from 17 patients and 19 potential carriers from the staff were collected from March 2007 to February 2008 and analyzed by pulsed-field gel electrophoresis (PFGE) to determine their clonal relationships. During this period the hospital reported 16 cases of hospital-acquired staphylococcal pneumonia and an apparent outbreak occurred from June to September 2007. DNA from these isolates formed six different PFGE patterns: four clonal groups, and two groups of clonally related isolates. Molecular typing failed to identify any staphylococcal reservoir among staff members. The current study suggested that a staphylococcal outbreak that occurred in the summer of 2007 was caused by different bacterial clones, although some clones were shared by two patients. Historical analysis of the staphylococcal infections in the ICU showed a higher incidence during the summer months, which coincided with the programmed personnel shift. This observation suggests that outbreaks might be produced by the introduction of improperly trained personnel.

The role of pDC, recipient T(reg) and donor T(reg) in HSC engraftment: Mechanisms of facilitation.

Hematopoietic stem cell transplantation (HSCT) has been utilized for treatment of many hematologic malignancies, genetic and metabolic disorders, and hemoglobinopathies such as sickle cell disease and thalassemia. It also induces donor-specific tolerance to organ and tissue transplants. The widespread success of HSCT is hampered by the toxicities of immunosuppression and development of graft-versus-host disease (GVHD). The mechanism of induction of transplantation tolerance (reciprocal donor/host) is still an elusive challenge in allogeneic HSCT. An understanding of the mechanisms for induction of tolerance and the critical cells involved in this process has resulted in novel cell-based therapies poised to be translated to clinical application. The focus of this review is those cells of interest.Bone marrow-derived plasmacytoid dendritic cells induce naïve T cells to differentiate to become antigen-specific regulatory T cells (T(reg)), creating a milieu for the induction of transplantation tolerance. Recently, CD8(+)/TCR(-) facilitating cells (FC), a novel cell population in mouse bone marrow, have been shown to potently enhance engraftment of allogeneic HSC without causing GVHD. The predominant subpopulation of FC resembles plasmacytoid precursor dendritic cells. FC induce antigen-specific T(reg) in vivo. Notably, FC address one major concern that has prevented the implementation of T(reg) cell therapy in the clinic: to expand T(reg) and have them remain tolerogenic in vivo. FC are novel in that they induce an antigen-specific regulatory milieu in vivo. The discovery of FC has opened new alternatives to expanded criteria in bone marrow transplantation that were previously restricted to human leukocyte antigen-matched recipients. The focus of this review is to cover what is currently known about the mechanism of FC action in inducing tolerance and preventing GVHD and hostversus-graft reactivity.