Mayra Alejandra Machuca

Respiratory syncytial virus (RSV) and rhinovirus (RV) are major causes of acute respiratory infections (ARIs) worldwide. The circulation of both RSV and RV was notably altered during the COVID-19 pandemic. This study analyzed the epidemiological and molecular characteristics of RSV and RV in Santander, Colombia, during the pandemic period (PP, 2020–2021) and the post-pandemic period (PPP, 2023–2024). A total of 921 respiratory samples from patients with ARIs were screened for RSV-A/B and RV. Sequences of the RSV attachment glycoprotein (G) gene and the RV VP4–VP2 region were analyzed in positive samples. Epidemiological and clinical characteristics of the study population were also assessed. RSV was not detected during PP, whereas RV was detected in 4.8% of samples. During PPP, RSV-A, RSV-B, and RV were detected in 5.6%, 4.4%, and 28.0% of samples, respectively. RSV infections were mainly identified in children, while RV was detected across all age groups. RSV-A sequences grouped within seven A.D-derived lineages (A.D.1.5, A.D.1.7, A.D.1.8, A.D.3.2, A.D.3.3, A.D.5.1, A.D.5.2), whereas RSV-B sequences clustered within the B.D.E.1 lineage. RV showed a higher number of detected genotypes during the PPP than during the PP. The genotypic characterization performed in this study provides new insight into the molecular epidemiology of RSV and RV in Santander, Colombia, during PP and PPP, and represents, to our knowledge, the first regional description of RSV lineages and RV genotypes across these periods.

Introduction. The emergence of antibiotic resistance in Escherichia coli has contributed to the increasing incidence and lethality of urinary tract infections. Objective. To characterize uropathogenic E. coli isolates obtained from patients with urinary tract infections in two hospitals in Bucaramanga, Colombia. Specifically, we assessed the significance of CRISPR 2.1 locus elements as a target for genotyping.Materials and methods. We combined phylotyping based on the Clermont classification, antimicrobial susceptibility testing approaches, and PCR amplification of the CRISPR 2.1 array.Results. We found that the variation in the CRISPR 2.1 array, along with the presence of resistance and virulence genes, phylogroups, and antibiotic sensitivity patterns provide significant and reliable data for epidemiological studies. The analysis of 72 isolates revealed considerable resistance to ampicillin and trimethoprim/sulfamethoxazole, with rates of 80% and 60%, respectively. The isolates also demonstrated the occurrence of blaCTX-M, blaTEM, and blaSHV genes in 54.55, 18.18, and 4.17% of the cases, respectively. According to the Clermont classification, groups D and B2 accounted for 65.2% of all isolates. The CRISPR 2.1 array was present in most isolates except those in group B2 and exhibited length polymorphism.Conclusions. Our results emphasized the utility of CRISPR 2.1 array polymorphism in reliably identifying uropathogenic E. coli and enhancing distinction, which is a noteworthy advance in regional epidemiological monitoring systems.

Introducción: Las infecciones respiratorias agudas (IRA) causadas por virus respiratorios constituyen una fuente importante de morbilidad y mortalidad en el mundo. Nos propusimos determinar la prevalencia de virus respiratorios en pacientes con sospecha de infección por SARS-CoV-2 y explorar la asociación entre coinfección de SARS-CoV-2 con otros virus respiratorios con la gravedad de la enfermedad respiratoria aguda. Métodos: Estudio de corte transversal, se analizaron hisopados de pacientes con síntomas sugestivos de COVID-19 en Santander, Colombia. Se seleccionaron muestras positivas y negativas para SARS-CoV-2 mediante un muestreo probabilístico proporcional. La detección de 15 virus se realizó mediante RT-qPCR en hisopados almacenados a -80°C. Se tomaron datos clínicos y epidemiológicos de las fichas epidemiológicas remitidas junto con la muestra respiratoria, para establecer la condición de gravedad (hospitalización o muerte por IRA). Resultados: Se incluyeron 600 hisopados colectados entre abril del 2020 y noviembre del 2021. La mediana de edad de los pacientes fue 55,0 años [RIC: 34,0] y el 58,5% fueron hombres. La prevalencia de rinovirus y adenovirus C fue de 4,7% y 0,3%, respectivamente. La prevalencia de coinfección de SARS-CoV-2 con rinovirus y adenovirus C fue de 3,3% (IC95%: 1,7-5,5) y 0,3% (IC95%: 0,0-1,4), respectivamente. Al momento de la toma de muestras, el 30,2 % correspondía a pacientes ambulatorios, el 59,8 % a pacientes hospitalizados y el 10,0 % a casos fatales. Se observó una diferencia en el reporte de comorbilidades entre los casos y controles (61,0 % vs. 46,5 %; p = 0,012). No se encontró asociación entre coinfección y la gravedad de la enfermedad (OR: 1,01; IC95%: 0,33 - 3,10), ajustando por edad, sexo, seguridad social y comorbilidades. Conclusiones: Durante el periodo epidémico la circulación de otros virus respiratorios fue baja. No observamos una asociación entre coinfección y gravedad de la enfermedad en las muestras evaluadas.

Patógenos ID es un recurso creado para los estudiantes de Microbiología y Bioanálisis que facilita la comprensión de las pruebas de laboratorio. Las cuales son usadas para identificar patógenos como los Enterobacterales y bacilos Gram negativos no fermentadores. El Objeto Virtual de Aprendizaje (OVA) es utilizado durante las horas de trabajo independiente para revisar el tema y como material de apoyo durante las prácticas de laboratorio. Patogenos ID is a resource created for Microbiology and Bioanalysis students that facilitates the understanding of laboratory tests. It is designed to identify pathogens of great medical importance like Enterobacterales and non-fermenting Gram-negative bacilli. The Virtual Learning Object (VLO) is used during independent work hours to review the subject, and as support material in the classroom during laboratory practices.

Chemotaxis is an important virulence factor of the foodborne pathogen Campylobacter jejuni. Inactivation of chemoreceptor Tlp3 reduces the ability of C. jejuni to invade human and chicken cells and to colonise the jejunal mucosa of mice. Knowledge of the structure of the ligand-binding domain (LBD) of Tlp3 in complex with its ligands is essential for a full understanding of the molecular recognition underpinning chemotaxis. To date, the only structure in complex with a signal molecule is Tlp3 LBD bound to isoleucine. Here, we used in vitro and in silico screening to identify eight additional small molecules that signal through Tlp3 as attractants by directly binding to its LBD, and determined the crystal structures of their complexes. All new ligands (leucine, valine, α-amino-N-valeric acid, 4-methylisoleucine, β-methylnorleucine, 3-methylisoleucine, alanine, and phenylalanine) are nonpolar amino acids chemically and structurally similar to isoleucine. X-ray crystallographic analysis revealed the hydrophobic side-chain binding pocket and conserved protein residues that interact with the ammonium and carboxylate groups of the ligands determine the specificity of this chemoreceptor. The uptake of hydrophobic amino acids plays an important role in intestinal colonisation by C. jejuni, and our study suggests that C. jejuni seeks out hydrophobic amino acids using chemotaxis.