CoVEx: SARS-CoV-2 Mutation Explorer for genomic surveillance.

Effective management of emerging diseases relies on timely pathogen identification and monitoring. The emergence of COVID-19 in December 2019, rapidly evolved into a global pandemic, with millions of cases and deaths reported worldwide. The accumulation of SARS-CoV-2 genomes provided unprecedented opportunities for studying the virus's evolutionary dynamics, understanding the impact of mutations, and identifying emerging Variants of Interest (VOIs) and Variants of Concern (VOCs).

Assessment of the shock index in septic shock: A systematic review.

Objective: To identify published research on the Shock Index (SI) in patients with septic shock or severe sepsis and to describe its main findings and conclusions.

Design: Systematic review of the literature following the recommendations of the PRISMA protocol (Preferred Reporting Items for Systematic Reviews and Meta-Analyses).

Settings: The following databases were consulted: Pubmed, Embase, Library Cochrane and Lilacs.

A 6-year retrospective study of clinical features, microbiology, and genomics of Shiga toxin-producing in children who presented to a tertiary referral hospital in Costa Rica.

Shiga-toxin-producing (STEC) is associated with diarrhea and hemolytic uremic syndrome (HUS). STEC infections in Costa Rica are rarely reported in children. We gathered all the records of STEC infections in children documented at the National Children's Hospital, a tertiary referral hospital, from 2015 to 2020.

Genome-Based Characterization of Listeria monocytogenes, Costa Rica.

Genomic data on the foodborne pathogen Listeria monocytogenes from Central America are scarce. We analyzed 92 isolates collected during 2009-2019 from different regions in Costa Rica, compared those to publicly available genomes, and identified unrecognized outbreaks. Our findings suggest mandatory reporting of listeriosis in Costa Rica would improve pathogen surveillance.

Overview of the SARS-CoV-2 genotypes circulating in Latin America during 2021.

Latin America is one of the regions in which the COVID-19 pandemic has a stronger impact, with more than 72 million reported infections and 1.6 million deaths until June 2022. Since this region is ecologically diverse and is affected by enormous social inequalities, efforts to identify genomic patterns of the circulating SARS-CoV-2 genotypes are necessary for the suitable management of the pandemic.

Nanoindentation Response of 3D Printed PEGDA Hydrogels in a Hydrated Environment.

Hydrogels are commonly used materials in tissue engineering and organ-on-chip devices. This study investigated the nanomechanical properties of monolithic and multilayered poly(ethylene glycol) diacrylate (PEGDA) hydrogels manufactured using bulk polymerization and layer-by-layer projection lithography processes, respectively. An increase in the number of layers (or reduction in layer thickness) from 1 to 8 and further to 60 results in a reduction in the elastic modulus from 5.

Clinical Profiles at the Time of Diagnosis of SARS-CoV-2 Infection in Costa Rica During the Pre-vaccination Period Using a Machine Learning Approach.

Unlabelled: The clinical manifestations of COVID-19, caused by the SARS-CoV-2, define a large spectrum of symptoms that are mainly dependent on the human host conditions. In Costa Rica, more than 169,000 cases and 2185 deaths were reported during the year 2020, the pre-vaccination period. To describe the clinical presentations at the time of diagnosis of SARS-CoV-2 infection in Costa Rica during the pre-vaccination period, we implemented a symptom-based clustering using machine learning to identify clusters or clinical profiles at the population level among 18,974 records of positive cases.

Metagenomic pipeline for identifying co-infections among distinct SARS-CoV-2 variants of concern: study cases from Alpha to Omicron.

Concomitant infection or co-infection with distinct SARS-CoV-2 genotypes has been reported as part of the epidemiological surveillance of the COVID-19 pandemic. In the context of the spread of more transmissible variants during 2021, co-infections are not only important due to the possible changes in the clinical outcome, but also the chance to generate new genotypes by recombination. However, a few approaches have developed bioinformatic pipelines to identify co-infections.

Antimicrobial Resistance and Genetic Diversity of Campylobacter spp. Isolated from Broiler Chicken at Three Levels of the Poultry Production Chain in Costa Rica.

Abstract: Campylobacter spp. are considered the most common bacterial cause of human gastroenteritis, one of the four main causes of diarrheal disease worldwide, and they are one of the main foodborne pathogens causing hospitalizations and deaths. Here, 148 strains of Campylobacter spp.

First Report of a Multidrug-Resistant ST58 Harboring Extended-Spectrum Beta-Lactamase of the CTX-M-1 Class in a Fecal Sample of a Captive Baird's Tapir () in Costa Rica, Central America.

This study's main objective was to analyze the antibiotic susceptibility profile of isolates obtained from a fecal sample of a captive Baird's tapir () in Costa Rica. The fecal sample was collected inside the enclosure on March 3, 2017, right after the animal defecated. Samples were cultured on MacConkey agar plates nonsupplemented and supplemented with 2 μg/mL of cefotaxime.

SARS-CoV-2 genomic surveillance in Costa Rica: Evidence of a divergent population and an increased detection of a spike T1117I mutation.

Genome sequencing is a key strategy in the surveillance of SARS-CoV-2, the virus responsible for the COVID-19 pandemic. Latin America is the hardest-hit region of the world, accumulating almost 20% of COVID-19 cases worldwide. In Costa Rica, from the first detected case on March 6th to December 31st almost 170,000 cases have been reported.

Whole genome sequencing of Shigella sonnei through PulseNet Latin America and Caribbean: advancing global surveillance of foodborne illnesses.

Objectives: Shigella sonnei is a globally important diarrhoeal pathogen tracked through the surveillance network PulseNet Latin America and Caribbean (PNLA&C), which participates in PulseNet International. PNLA&C laboratories use common molecular techniques to track pathogens causing foodborne illness. We aimed to demonstrate the possibility and advantages of transitioning to whole genome sequencing (WGS) for surveillance within existing networks across a continent where S.

SALMATcor: microagglutination for Salmonella flagella serotyping.

Salmonella is a complex bacterial group with more than 2400 serovars widely distributed in nature; they are considered zoonotic because they can infect a variety of animals and be transmitted to humans. Usually, they cause alimentary acquired diseases such as gastroenteritis, typhoid fever, and others that can lead to severe complications and death. Serotyping is useful to differentiate among Salmonella, because it shows an important correlation with their clinical and epidemiological patterns; consequently, it is of high value for public health, animal health, agriculture, and industry.