The Immunopeptidomics Ontology (ImPO).

The adaptive immune response plays a vital role in eliminating infected and aberrant cells from the body. This process hinges on the presentation of short peptides by major histocompatibility complex Class I molecules on the cell surface. Immunopeptidomics, the study of peptides displayed on cells, delves into the wide variety of these peptides. Understanding the mechanisms behind antigen processing and presentation is crucial for effectively evaluating cancer immunotherapies. As an emerging domain, immunopeptidomics currently lacks standardization-there is neither an established terminology nor formally defined semantics-a critical concern considering the complexity, heterogeneity, and growing volume of data involved in immunopeptidomics studies. Additionally, there is a disconnection between how the proteomics community delivers the information about antigen presentation and its uptake by the clinical genomics community. Considering the significant relevance of immunopeptidomics in cancer, this shortcoming must be addressed to bridge the gap between research and clinical practice. In this work, we detail the development of the ImmunoPeptidomics Ontology, ImPO, the first effort at standardizing the terminology and semantics in the domain. ImPO aims to encapsulate and systematize data generated by immunopeptidomics experimental processes and bioinformatics analysis. ImPO establishes cross-references to 24 relevant ontologies, including the National Cancer Institute Thesaurus, Mondo Disease Ontology, Logical Observation Identifier Names and Codes and Experimental Factor Ontology. Although ImPO was developed using expert knowledge to characterize a large and representative data collection, it may be readily used to encode other datasets within the domain. Ultimately, ImPO facilitates data integration and analysis, enabling querying, inference and knowledge generation and importantly bridging the gap between the clinical proteomics and genomics communities. As the field of immunogenomics uses protein-level immunopeptidomics data, we expect ImPO to play a key role in supporting a rich and standardized description of the large-scale data that emerging high-throughput technologies are expected to bring in the near future. Ontology URL: https://zenodo.org/record/10237571 Project GitHub: https://github.com/liseda-lab/ImPO/blob/main/ImPO.owl.

Diecinueve años de vigilancia de enfermedad invasiva neumocócica en un hospital pediátrico de Mendoza, Argentina / Nineteen-years of pneumococcal invasive disease surveillance in a children’s hospital in Mendoza, Argentina

Estudiamos 537 niños internados en el Hospital Dr. Notti, entre 1993 y 2011, con enfermedad invasiva neumocócica. La mediana de edad fue 19 meses (R = 0-192 m); 34,82% fueron < 1 año y 23,46%, t 60 meses. Predominaron neumonía con y sin derrame (48,04%) y meningitis (29,05%), con una letalidad de 6,14%. El 56,86% de los serotipos identificados fueron 14, 5 y 1. Mostraron sensibilidad a la penicilina el 99,74% de cepas no meníngeas y a la ceftriaxona, el 98,08% de cepas meníngeas. Los factores de riesgo en neumonía con derrame se asociaron a la edad t 60 meses, RR 1,47 (1,06-2,04), p 0,02, serotipos 5, RR 2,57 (1,71-3,87), p 0,0001 y 1 RR 1,86 (1,17-2,96), p 0,014 y en las meningitis, principalmente a < 1 año, RR 2,35 (1,87-3,06), p 0,0000 y serotipo 18C, RR 2,19 (1,3-3,7), p 0,024. Conclusión. El Streptococcus pneumoniae representó un problema importante en menores de un año, en quienes predominó la meningitis y causó más de la mitad de las muertes, y en mayores de 60 meses, en los que prevalecieron neumonías con derrame. La mayoría fueron sensibles a la penicilina y a la ceftriaxona.

Five hundred and thirty-seven children admitted to Hospital Dr. Notti and diagnosed with invasive pneumococcal disease between 1993 and 2011 were studied. Their median age was 19 months (range= 0-192 months); 34.82% were <1 year old and 23.46%, ≥60 months old. Pneumonia with or without effusion (48.04%) and meningitis (29.05%) were the most predominant conditions, with a case fatality rate of 6.14%. Identified serotypes corresponded to 14, 5 and 1 in 56.86% of cases. Sensitivity to penicillin was observed in 99.74% of non-meningeal strains, while sensitivity to ceftriaxone was found in 98.08% of meningeal strains. Risk factors in pneumonia with effusion were associated to age ≥60 months old, RR: 1.47 (1.06-2.04), p= 0.02, to serotype 5, RR: 2.57 (1.71-3.87), p= 0.0001, and to serotype 1, RR: 1.86 (1.17-2.96), p= 0.014; in the case of meningitis, risk factors were mainly associated to age <1 year old, RR: 2.35 (1.87-3.06), p= 0.0000, and to serotype 18C, RR: 2.19 (1.3-3.7), p= 0.024. Conclusion. Streptococcus pneumonia was a major problem in infants younger than one year old, who predominantly developed meningitis which caused half of deaths, and in children older than 60 months old, who had a prevalence of pneumonia with effusion. Most cases were sensitive to penicillin and ceftriaxone

Nineteen-years of pneumococcal invasive disease surveillance in a children's hospital in Mendoza, Argentina.

Five hundred and thirty-seven children admitted to Hospital Dr. Notti and diagnosed with invasive pneumococcal disease between 1993 and 2011 were studied. Their median age was 19 months (range= 0-192 months); 34.82% were <1 year old and 23.46%, >60 months old. Pneumonia with or without effusion (48.04%) and meningitis (29.05%) were the most predominant conditions, with a case fatality rate of 6.14%. Identified serotypes corresponded to 14, 5 and 1 in56.86% of cases. Sensitivity to penicillin was observed in99.74% of non-meningeal strains, while sensitivity to ceftriaxone was found in 98.08% ofmeningeal strains. Risk factors inpneumonia with effusionwere associated to age >60 months old, RR: 1.47 (1.06-2.04), p= 0.02, to serotype 5, RR: 2.57 (1.71-3.87), p= 0.0001, and to serotype 1, RR: 1.86 (1.17-2.96), p= 0.014; in the case of meningitis, risk factors were mainly associated to age <1 year old, RR: 2.35 (1.87-3.06), p= 0.0000, and to serotype 18C, RR: 2.19 (1.3-3.7), p= 0.024. Conclusion. Streptococcus pneumonia was a major problem in infants younger than one year old, who predominantly developed meningitis which caused half of deaths, and in children older than 60 months old, who had a prevalence of pneumonia with effusion. Most cases were sensitive to penicillin and ceftriaxone.

Nineteen-years of pneumococcal invasive disease surveillance in a childrens hospital in Mendoza, Argentina. / Nineteen-years of pneumococcal invasive disease surveillance in a childrens hospital in Mendoza, Argentina.

Five hundred and thirty-seven children admitted to Hospital Dr. Notti and diagnosed with invasive pneumococcal disease between 1993 and 2011 were studied. Their median age was 19 months (range= 0-192 months); 34.82

were <1 year old and 23.46

, >60 months old. Pneumonia with or without effusion (48.04

) and meningitis (29.05

) were the most predominant conditions, with a case fatality rate of 6.14

. Identified serotypes corresponded to 14, 5 and 1 in56.86

of cases. Sensitivity to penicillin was observed in99.74

of non-meningeal strains, while sensitivity to ceftriaxone was found in 98.08

ofmeningeal strains. Risk factors inpneumonia with effusionwere associated to age >60 months old, RR: 1.47 (1.06-2.04), p= 0.02, to serotype 5, RR: 2.57 (1.71-3.87), p= 0.0001, and to serotype 1, RR: 1.86 (1.17-2.96), p= 0.014; in the case of meningitis, risk factors were mainly associated to age <1 year old, RR: 2.35 (1.87-3.06), p= 0.0000, and to serotype 18C, RR: 2.19 (1.3-3.7), p= 0.024. Conclusion. Streptococcus pneumonia was a major problem in infants younger than one year old, who predominantly developed meningitis which caused half of deaths, and in children older than 60 months old, who had a prevalence of pneumonia with effusion. Most cases were sensitive to penicillin and ceftriaxone.

Risk factors for sporadic Shiga toxin-producing Escherichia coli infections in children, Argentina.

We evaluated risk factors for sporadic Shiga toxin-producing Escherichia coli (STEC) infection among children in Argentina. We conducted a prospective case-control study in 2 sites and enrolled 150 case-patients and 299 controls. The median age of case-patients was 1.8 years; 58% were girls. Serotype O157:H7 was the most commonly isolated STEC. Exposures associated with infection included eating undercooked beef, living in or visiting a place with farm animals, and contact with a child <5 years of age with diarrhea. Protective factors included the respondent reporting that he or she always washed hands after handling raw beef and the child eating more than the median number of fruits and vegetables. Many STEC infections in children could be prevented by avoiding consumption of undercooked beef, limiting exposure to farm animals and their environment, not being exposed to children with diarrhea, and washing hands after handling raw beef.

Intestinal bleeding and occlusion associated with shiga toxin-producing Escherichia coli 0127: H21

We report a case of a nine-year old boy with vomiting, abdominal pain and fever, who underwent surgery with a diagnosis of appendicitis in Mendonza and from whom a Shiga toxin-producing Escherichia coli (STEC) 0127:H21 strain was recovered. Forty-eight hours after surgery he presented bilious vomiting and two episodes of intestinal bleeding. Loboratory findings included: hematocrit, 35 per cent; blood urea nitrogen, 0.22 g/L. The urinary output was normal. The following day physical examination showed an alert mildy hydrated child, without fever but with distended and painful abdomen. The patient was again submitted to surgery with a diagnosis of intestinal occlusion. Bleeding and multiple adhesions in jejunum and ileum were found. The patient still had tense and painful abdomen and presented two bowel movements with blood; hematocrit fell to 29 per cent and blood urea nitrogen rose to 0.32 g/L. STEC 0127:H21 eae(-)/Stx2/Stx2vh-b(+)/E-Hly(+) was isolated from a stool sample. He was discharged after 10 days of hospitalization and no long-term complications such as HUS or TTP were observed. This is the first report, to our knoweledge, on the isolation of E.coli 0127:H21, carrying the virulence factors that characterize STEC strains, associated to an enterohemorrhagic colitis case. This serotype was previously characterized as a non-classic enteropathogenic E. coli (EPEC). STEC infections can mimic infectious or noninfectious pathologies. Therefore an important aspect of clinical managements is making the diagnosis using different criteria thereby avoiding misdiagnoses which have occasionally led to invasive diagnostic and therapeutic procedures or the inappropriate use of antibiotics.

Intestinal bleeding and occlusion associated with shiga toxin-producing Escherichia coli 0127: H21

We report a case of a nine-year old boy with vomiting, abdominal pain and fever, who underwent surgery with a diagnosis of appendicitis in Mendonza and from whom a Shiga toxin-producing Escherichia coli (STEC) 0127:H21 strain was recovered. Forty-eight hours after surgery he presented bilious vomiting and two episodes of intestinal bleeding. Loboratory findings included: hematocrit, 35 per cent; blood urea nitrogen, 0.22 g/L. The urinary output was normal. The following day physical examination showed an alert mildy hydrated child, without fever but with distended and painful abdomen. The patient was again submitted to surgery with a diagnosis of intestinal occlusion. Bleeding and multiple adhesions in jejunum and ileum were found. The patient still had tense and painful abdomen and presented two bowel movements with blood; hematocrit fell to 29 per cent and blood urea nitrogen rose to 0.32 g/L. STEC 0127:H21 eae(-)/Stx2/Stx2vh-b(+)/E-Hly(+) was isolated from a stool sample. He was discharged after 10 days of hospitalization and no long-term complications such as HUS or TTP were observed. This is the first report, to our knoweledge, on the isolation of E.coli 0127:H21, carrying the virulence factors that characterize STEC strains, associated to an enterohemorrhagic colitis case. This serotype was previously characterized as a non-classic enteropathogenic E. coli (EPEC). STEC infections can mimic infectious or noninfectious pathologies. Therefore an important aspect of clinical managements is making the diagnosis using different criteria thereby avoiding misdiagnoses which have occasionally led to invasive diagnostic and therapeutic procedures or the inappropriate use of antibiotics. (AU)

Sindrome uremico hemolitico en niños de Mendoza, Argentina: asociacion con la infeccion por Escherichia coli productor de toxina Shiga / Hemolytic uremic syndrome in children of Mendoza, Argentina: association with Shiga toxin-producing Escherichia coli infection

Escherichia coli productor de toxina Shiga (STEC) ha sido asociado con la etiopatogenia del síndrome urémico hemolítico (SUH). El objetivo fue caracterizar los casos de SUH observados en Mendoza y determinar su asociación con la infección por STEC. Entre el 1º de Julio de 1994 y el 30 de Junio de 1996 ingresaron al Hospital Pediátrico "Dr. HJ Notti", 36 pacientes con diagnóstico de SUH. La edad promedio fue de 22.8 meses, con un 44 por ciento en el sexo femenino. La enfermedad se estableció después de un período prodrómico de 4.5 días, el 94.4 por ciento de los pacientes presentó diarrea siendo sanguinolenta en el 83.3 por ciento de los casos. El 69.4 por ciento recibió antibioticoterapia antes de su ingreso. Los casos se presentaron fundamentalmente en niños eutróficos (88.9 por ciento), de condición socioeconómica media-baja (91.7 por ciento) de origem urbano (72.2 por ciento), durante el verano y principios de otoño. En el período de estado los pacientes presentaron palidez (100 por ciento), edema (25 por ciento), anuria (38.9 por ciento), oliguria (41.7 por ciento), anemia hemolítica (97.2 por ciento), trombocitopenia (86.1 por ciento) y compromiso neurológico (41.7 por ciento). Veinticinco pacientes presentaron formas completas de SUH. El 50 por ciento de los pacientes fue dializado y el 88.9 por ciento requirió transfusión de sedimento globular. El promedio de días de internación fue de 15.1. El 91.7 por ciento de los pacientes recuperó la función renal, dos pacientes evolucionaron a insuficiencia renal crónica y uno falleció. Evidencias acumulativas de infección por STEC se encontraron en 19 (86.4 por ciento) de 22 pacientes, STEC del serotipo 0157:H7, biotipo C fue detectado en 8 casos (36.4 por ciento). Stx2 fue la citotoxina prevalente en STEC, en materia fecal (STMF) y anticuerpos a-Stx.

Sindrome uremico hemolitico en niños de Mendoza, Argentina: asociacion con la infeccion por Escherichia coli productor de toxina Shiga / Hemolytic uremic syndrome in children of Mendoza, Argentina: association with Shiga toxin-producing Escherichia coli infection

Escherichia coli productor de toxina Shiga (STEC) ha sido asociado con la etiopatogenia del síndrome urémico hemolítico (SUH). El objetivo fue caracterizar los casos de SUH observados en Mendoza y determinar su asociación con la infección por STEC. Entre el 1º de Julio de 1994 y el 30 de Junio de 1996 ingresaron al Hospital Pediátrico "Dr. HJ Notti", 36 pacientes con diagnóstico de SUH. La edad promedio fue de 22.8 meses, con un 44 por ciento en el sexo femenino. La enfermedad se estableció después de un perío