Hybrid capture shotgun sequencing detected unexpected viruses in the cerebrospinal fluid of children with acute meningitis and encephalitis.

PURPOSE: Investigation of undiagnosed cases of infectious neurological diseases, especially in the paediatric population, remains a challenge. This study aimed to enhance understanding of viruses in CSF from children with clinically diagnosed meningitis and/or encephalitis (M/ME) of unknown aetiology using shotgun sequencing enhanced by hybrid capture (HCSS). METHODS: A single-centre prospective study was conducted at Sant Joan de Déu University Hospital, Barcelona, involving 40 M/ME episodes of unknown aetiology, recruited from May 2021 to July 2022. All participants had previously tested negative with the FilmArray Meningitis/Encephalitis Panel. HCSS was used to detect viral nucleic acid in the patients' CSF. Sequencing was performed on Illumina NovaSeq platform. Raw sequence data were analysed using CZ ID metagenomics and PikaVirus bioinformatics pipelines. RESULTS: Forty episodes of M/ME of unknown aetiology in 39 children were analysed by HCSS. A significant viral detection in 30 CSF samples was obtained, including six parechovirus A, three enterovirus ACD, four polyomavirus 5, three HHV-7, two BKV, one HSV-1, one VZV, two CMV, one EBV, one influenza A virus, one rhinovirus, and 13 HERV-K113 detections. Of these, one sample with BKV, three with HHV-7, one with EBV, and all HERV-K113 were confirmed by specific PCR. The requirement for Intensive Care Unit admission was associated with HCSS detections. CONCLUSION: This study highlights HCSS as a powerful tool for the investigation of undiagnosed cases of M/ME. Data generated must be carefully analysed and reasonable precautions must be taken before establishing association of clinical features with unexpected or novel virus findings.

Characteristics and Risk Factors Associated with SARS-CoV-2 Pneumonias in Hospitalized Pediatric Patients: A Pilot Study.

SARS-CoV-2 pneumonia in children has a lower incidence and severity compared to adults. Risk factors are adolescence and comorbidities. Our aims were to describe the characteristics of children admitted with SARS-CoV-2 pneumonia, identify risk factors associated with severity and compare the cases according to the variant of SARS-CoV-2. This was a descriptive and retrospective study, including patients aged 0-18 years hospitalized in a tertiary-care hospital between 1 March 2020 and 1 March 2022. Epidemiological, clinical, diagnostic and therapeutic data were analyzed. Forty-four patients were admitted; twenty-six (59%) were male and twenty-seven (61%) were older than 12 years. Thirty-six (82%) had comorbidities, the most frequent of which were obesity and asthma. Seven (15.9%) patients required high-flow oxygen, eleven (25%) non-invasive ventilation and four (9.1%) conventional mechanical ventilation. In critically ill patients, higher levels of anemia, lymphopenia, procalcitonin, lactate dehydrogenase (LDH) and hypoalbuminemia and lower levels of HDL-cholesterol were detected (all p < 0.05). Prematurity (p = 0.022) was associated with intensive care unit admission. Patients were younger during the Omicron wave (p < 0.01); no variant was associated with greater severity. In conclusion, pediatric patients with a history of prematurity or with anemia, lymphopenia, elevated procalcitonin, elevated LDH levels, hypoalbuminemia and low HDL-cholesterol levels may require admission and present more severe forms. Apart from age, no notable differences between SARS-CoV-2 variant periods were found.

Nirsevimab para la prevención de la enfermedad por virus respiratorio sincitial en niños. Posicionamiento de la Sociedad Española de Infectología Pediátrica / Nirsevimab for the prevention of respiratory syncytial virus disease in children: Statement of the Spanish Society of Paediatric Infectious Disease (SEIP)

Introducción: Recientemente se ha aprobado en Europa y en España el uso de nirsevimab, un anticuerpo monoclonal (AcM) para la prevención de la enfermedad por virus respiratorio sincitial (VRS). Objetivos: Facilitar unas recomendaciones para la administración de nirsevimab para la prevención de la enfermedad por VRS. Métodos: Para la elaboración de estas recomendaciones, se decidió realizar una revisión crítica de la literatura, utilizando la metodología Delphi y la metodología GRADE. Se definió un grupo de expertos. Se realizaron tres rondas para definir las preguntas, manifestarse a favor o en contra, graduar la recomendación, y definir el acuerdo o el desacuerdo con las conclusiones. Resultados: En la población general de recién nacidos, se recomienda administrar rutinariamente nirsevimab para reducir la enfermedad y la hospitalización por bronquiolitis y enfermedad de vías bajas por VRS. Se recomienda administrar nirsevimab a todos los lactantes que nazcan en la estación de alta incidencia de VRS y aquellos que cuando esta comience, tengan menos de seis meses de edad. En los pacientes prematuros de 29 a 35 semanas de edad gestacional, en los lactantes con cardiopatía hemodinámicamente significativa y lactantes con enfermedad pulmonar crónica se recomienda rutinariamente administrar nirsevimab para reducir la enfermedad y la hospitalización por bronquiolitis y enfermedad de vías bajas por VRS. En los pacientes con indicación actual de palivizumab, se recomienda sustituir palivizumab por nirsevimab para reducir la carga de enfermedad de bronquiolitis. Conclusiones: Se recomienda administrar rutinariamente nirsevimab a todos los recién nacidos menores de seis meses nacidos en la estación de VRS o que tengan menos de seis meses cuando entran en la estación invernal, para reducir la carga de enfermedad y la hospitalización por bronquiolitis. (AU)

Introduction: Nirsevimab, a monoclonal antibody for the prevention of disease caused by respiratory syncytial virus (RSV), has recently been approved for use in Europe and Spain. Objectives: To provide recommendations for the administration of nirsevimab for prevention of RSV disease. Methods: The approach chosen to develop these recommendations involved a critical review of the literature and the use of the Delphi and GRADE methods. An expert group was formed. The group engaged in three rounds to define the questions, express support or opposition, grade recommendations and establish the agreement or disagreement with the conclusions. Results: In the general neonatal population, routine administration of nirsevimab is recommended to reduce the frequency of illness and hospitalisation for bronchiolitis and RSV lower respiratory tract infection. Nirsevimab is recommended for all infants born in high-incidence RSV season and infants aged less than 6 months at the season onset. In infants born preterm between 29 and 35 weeks of gestation, with haemodynamically significant heart disease or with chronic lung disease, routine administration of nirsevimab is recommended to reduce the incidence of disease and hospitalisation due to bronchiolitis and RSV lower respiratory tract infection. In patients in whom palivizumab is currently indicated, its substitution by nirsevimab is recommended to reduce the burden of bronchiolitis. Conclusions: Routine administration of nirsevimab to all infants aged less than 6 months born during the RSV season or aged less than 6 months at the start of the winter season is recommended to reduce the burden of disease and the frequency of hospitalization due to bronchiolitis. (AU)

Nirsevimab for the prevention of respiratory syncytial virus disease in children. Statement of the Spanish Society of Paediatric Infectious Disease (SEIP).

INTRODUCTION: Nirsevimab, a monoclonal antibody for the prevention of disease caused by respiratory syncytial virus (RSV), has recently been approved for use in Europe and Spain. OBJECTIVES: To provide recommendations for the administration of nirsevimab for prevention of RSV disease. METHODS: The approach chosen to develop these recommendations involved a critical review of the literature and the use of the Delphi and GRADE methods. An expert group was formed. The group engaged in three rounds to define the questions, express support or opposition, grade recommendations and establish the agreement or disagreement with the conclusions. RESULTS: In the general neonatal population, routine administration of nirsevimab is recommended to reduce the frequency of illness and hospitalisation for bronchiolitis and RSV lower respiratory tract infection. Nirsevimab is recommended for all infants born in high-incidence RSV season and infants aged less than 6 months at the season onset. In infants born preterm between 29 and 35 weeks of gestation, with haemodynamically significant heart disease or with chronic lung disease, routine administration of nirsevimab is recommended to reduce the incidence of disease and hospitalisation due to bronchiolitis and RSV lower respiratory tract infection. In patients in whom palivizumab is currently indicated, its substitution by nirsevimab is recommended to reduce the burden of bronchiolitis. CONCLUSIONS: Routine administration of nirsevimab to all infants aged less than 6 months born during the RSV season or aged less than 6 months at the start of the winter season is recommended to reduce the burden of disease and the frequency of hospitalization due to bronchiolitis.

Association between soluble angiotensin-converting enzyme 2 in saliva and SARS-CoV-2 infection: a cross-sectional study.

This study aimed to investigate the association between saliva soluble angiotensin-converting enzyme 2 (sACE2) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in children and adults. We selected a convenience sample of adults with post-acute SARS-CoV-2 infection and their household children living in quarantined family households of the metropolitan Barcelona region (Spain) during the spring 2020 pandemic national lockdown. Participants were tested for saliva sACE2 quantification by western blot and nasopharyngeal SARS-CoV-2 RT-PCR detection. A total of 161 saliva samples [82 (50.9%) from children; 79 (49.1%) from females] yielded valid western blot and RT-PCR results. Saliva sACE2 was detected in 79 (96.3%) children and 76 (96.2%) convalescent adults. Twenty (24.4%) children and 20 (25.3%) convalescent adults were positive for SARS-CoV-2 in nasopharynx by RT-PCR. SARS-CoV-2 RT-PCR-negative children had a significantly higher mean proportional level of saliva sACE2 (0.540 × 10-3%) than RT-PCR-positive children (0.192 × 10-3%, p < 0.001) and convalescent adults (0.173 × 10-3%, p < 0.001). In conclusion, children negative for nasopharyngeal SARS-CoV-2 RT-PCR appear to exhibit a higher concentration of saliva sACE2 than SARS-CoV-2 RT-PCR-positive children and convalescent adults. Release of adequate levels of sACE2 in saliva could play a protective role against SARS-CoV-2.

Impact of the bacterial nasopharyngeal microbiota on the severity of genus enterovirus lower respiratory tract infection in children: A case-control study.

INTRODUCTION: Rhinoviruses (RV) and enteroviruses (EV) are among the main causative etiologies of lower respiratory tract infection (LRTI) in children. The clinical spectrum of RV/EV infection is wide, which could be explained by diverse environmental, pathogen-, and host-related factors. Little is known about the nasopharyngeal microbiota as a risk factor or disease modifier for RV/EV infection in pediatric patients. This study describes distinct nasopharyngeal microbiota profiles according to RV/EV LRTI status in children. METHODS: Cross-sectional case-control study, conducted at Hospital Sant de Déu (Barcelona, Spain) from 2017 to 2020. Three groups of children <5 years were included: healthy controls without viral detection (Group A), mild or asymptomatic controls with RV/EV infection (Group B), and cases with severe RV/EV infection admitted to the pediatric intensive care unit (PICU) (Group C). Nasopharyngeal samples were collected from participants for viral DNA/RNA detection by multiplex-polymerase chain reaction and bacterial microbiota characterization by 16S rRNA gene sequencing. RESULTS: A total of 104 subjects were recruited (A = 17, B = 34, C = 53). Children's nasopharyngeal microbiota composition varied according to their RV/EV infection status. Richness and diversity were decreased among children with severe infection. Nasopharyngeal microbiota profiles enriched in genus Dolosigranulum were related to respiratory health, while genus Haemophilus was specifically predominant in children with severe RV/EV LRTI. Children with mild or asymptomatic RV/EV infection showed an intermediate profile. CONCLUSIONS: These results suggest a close relationship between the nasopharyngeal microbiota and different clinical presentations of RV/EV infection.

Acute and long-term immune responses to SARS-CoV-2 infection in unvaccinated children and young adults with inborn errors of immunity.

Purpose: To describe SARS-CoV-2 infection outcome in unvaccinated children and young adults with inborn errors of immunity (IEI) and to compare their specific acute and long-term immune responses with a sex-, age-, and severity-matched healthy population (HC). Methods: Unvaccinated IEI patients up to 22 years old infected with SARS-CoV-2 were recruited along with a cohort of HC. SARS-CoV-2 serology and ELISpot were performed in the acute phase of infection (up to 6 weeks) and at 3, 6, 9, and 12 months. Results: Twenty-five IEI patients (median age 14.3 years, min.-max. range 4.5-22.8; 15/25 males; syndromic combined immunodeficiencies: 48.0%, antibody deficiencies: 16.0%) and 17 HC (median age 15.3 years, min.-max. range 5.4-20.0; 6/17 males, 35.3%) were included. Pneumonia occurred in 4/25 IEI patients. In the acute phase SARS-CoV-2 specific immunoglobulins were positive in all HC but in only half of IEI in whom it could be measured (n=17/25): IgG+ 58.8% (10/17) (p=0.009); IgM+ 41.2% (7/17)(p<0.001); IgA+ 52.9% (9/17)(p=0.003). Quantitative response (index) was also lower compared with HC: IgG IEI (3.1 ± 4.4) vs. HC (3.5 ± 1.5)(p=0.06); IgM IEI (1.9 ± 2.4) vs. HC (3.9 ± 2.4)(p=0.007); IgA IEI (3.3 ± 4.7) vs. HC (4.6 ± 2.5)(p=0.04). ELISpots positivity was qualitatively lower in IEI vs. HC (S-ELISpot IEI: 3/11, 27.3% vs. HC: 10/11, 90.9%; p=0.008; N-ELISpot IEI: 3/9, 33.3% vs. HC: 11/11, 100%; p=0.002) and also quantitatively lower (S-ELISpot IEI: mean index 3.2 ± 5.0 vs. HC 21.2 ± 17.0; p=0.001; N-ELISpot IEI: mean index 9.3 ± 16.6 vs. HC: 39.1 ± 23.7; p=0.004). As for long term response, SARS-CoV-2-IgM+ at 6 months was qualitatively lower in IEI(3/8, 37.5% vs. 9/10 HC: 90.0%; p=0.043), and quantitatively lower in all serologies IgG, M, and A (IEI n=9, 1.1 ± 0.9 vs. HC n=10, 2.1 ± 0.9, p=0.03; IEI n=9, 1.3 ± 1.5 vs. HC n=10, 2.9 ± 2.8, p=0.02; and IEI n=9, 0.6 ± 0.5 vs. HC n=10, 1.7 ± 0.8, p=0.002 -respectively) but there were no differences at remaining time points. Conclusions: Our IEI pediatric cohort had a higher COVID-19 pneumonia rate than the general age-range population, with lower humoral and cellular responses in the acute phase (even lower compared to the reported IEI serological response after SARS-CoV-2 vaccination), and weaker humoral responses at 6 months after infection compared with HC.

Low transmission of SARS-CoV-2 derived from children in family clusters: An observational study of family households in the Barcelona Metropolitan Area, Spain.

BACKGROUND: Family clusters offer a good opportunity to study viral transmission in a stable setting. We aimed to analyze the specific role of children in transmission of SARS-CoV-2 within households. METHODS: A prospective, longitudinal, observational study, including children with documented acute SARS-CoV-2 infection attending 22 summer-schools in Barcelona, Spain, was performed. Moreover, other patients and families coming from other school-like environments that voluntarily accessed the study were also studied. A longitudinal follow-up (5 weeks) of the family clusters was conducted to determine whether the children considered to be primary cases were able to transmit the virus to other family members. The household reproduction number (Re*) and the secondary attack rate (SAR) were calculated. RESULTS: 1905 children from the summer schools were screened for SARS-CoV-2 infection and 22 (1.15%) tested positive. Moreover, 32 additional children accessed the study voluntarily. Of these, 37 children and their 26 households were studied completely. In half of the cases (13/26), the primary case was considered to be a child and secondary transmission to other members of the household was observed in 3/13, with a SAR of 14.2% and a Re* of 0.46. Conversely, the SAR of adult primary cases was 72.2% including the kids that gave rise to the contact tracing study, and 61.5% without them, and the estimated Re* was 2.6. In 4/13 of the paediatric primary cases (30.0%), nasopharyngeal PCR was persistently positive > 1 week after diagnosis, and 3/4 of these children infected another family member (p<0.01). CONCLUSIONS: Children may not be the main drivers of the infection in household transmission clusters in the study population. A prolonged positive PCR could be associated with higher transmissibility.

Safety and effectiveness of bubble continuous positive airway pressure as respiratory support for bronchiolitis in a pediatric ward.

The results of several clinical trials suggest that continuous positive airway pressure (CPAP) for acute bronchiolitis can be more effective than high-flow nasal cannula (HFNC). The use of HFNC involved a minimum reduction (5%) in admissions to the pediatric intensive care unit (PICU) in our hospital. Our main aim was to evaluate its safety and effectiveness as respiratory support for patients with bronchiolitis in a pediatric general ward. A secondary goal was to compare the admissions to PICU and the invasive mechanical ventilation (IMV) rate of patients treated with HFNC and those treated with HFNC/b-CPAP during the 2018-2019 and 2019-2020 epidemic seasons, respectively. Two prospective single-centre observational studies were performed. For the main aim, a cohort study (CS1) was carried out from 1st of November 2019 to 15th of January 2020. Inclusion criteria were children aged up to 3 months with bronchiolitis treated with b-CPAP support when HFNC failed. Epidemiological and clinical parameters were collected before and 60 min after the onset of CPAP and compared between the responder (R) and non-responders (NR) groups. NR was the group that required PICU admission. One hundred fifty-eight patients were admitted to the ward with bronchiolitis and HFNC. Fifty-seven out of one hundred fifty-eight required b-CPAP. No adverse events were observed. Thirty-two out of fifty-seven remained in the general ward (R-group), and 25/57 were admitted to PICU (NR-group). There were statistically significant differences in respiratory rate (RR) and heart rate (HR) between both groups before and after the initiation of b-CPAP, but the multivariable models showed that the main differences were observed after 60 min of therapy (lower HR, RR, BROSJOD score and FiO2 in the R-group). For the secondary aim, another cohort study (CS2) was performed comparing data from a pre-b-CPAP bronchiolitis season (1st of November 2018 to 15th January 2019) and the b-CPAP season (2019-2020). Inclusion criteria in pre-b-CPAP season were children aged up to 3 months admitted to the same general ward with moderate-severe bronchiolitis and with HFNC support. Admissions to PICU during the CPAP season were significantly reduced, without entailing an increase in the rate of IMV. CONCLUSION: The implementation of b-CPAP for patients with bronchiolitis in a pediatric ward, in whom HFNC fails, is safe and effective and results in a reduction in PICU admissions. WHAT IS KNOWN: • Bronchiolitis is one of the most frequent respiratory infections in children and one of the leading causes of hospitalization in infants. • Several studies suggest that the use of continuous positive airway pressure (CPAP) for acute bronchiolitis can be more effective than the high flow nasal cannula (HFNC). CPAP is a non-invasive ventilation (NIV) therapy used in patients admitted to pediatric intensive care unit (PICU) with progressive moderate-severe bronchiolitis. There is little experience in the literature on the use of continuous positive airway pressure (CPAP) for acute bronchiolitis in a general ward. WHAT IS NEW: • CPAP could be safely and effectively used as respiratory support in young infants with moderate-severe bronchiolitis in a general ward and it reduced the rate of patients who required PICU admission. • Patients' heart and respiratory rate and their FiO2 needs in the first 60 minutes may help to decide whether or not to continue the CPAP therapy in a general ward.

Impact of COVID-19 Lockdown on the Nasopharyngeal Microbiota of Children and Adults Self-Confined at Home.

The increased incidence of COVID-19 cases and deaths in Spain in March 2020 led to the declaration by the Spanish government of a state of emergency imposing strict confinement measures on the population. The objective of this study was to characterize the nasopharyngeal microbiota of children and adults and its relation to SARS-CoV-2 infection and COVID-19 severity during the pandemic lockdown in Spain. This cross-sectional study included family households located in metropolitan Barcelona, Spain, with one adult with a previous confirmed COVID-19 episode and one or more exposed co-habiting child contacts. Nasopharyngeal swabs were used to determine SARS-CoV-2 infection status, characterize the nasopharyngeal microbiota and determine common respiratory DNA/RNA viral co-infections. A total of 173 adult cases and 470 exposed children were included. Overall, a predominance of Corynebacterium and Dolosigranulum and a limited abundance of common pathobionts including Haemophilus and Streptococcus were found both among adults and children. Children with current SARS-CoV-2 infection presented higher bacterial richness and increased Fusobacterium, Streptococcus and Prevotella abundance than non-infected children. Among adults, persistent SARS-CoV-2 RNA was associated with an increased abundance of an unclassified member of the Actinomycetales order. COVID-19 severity was associated with increased Staphylococcus and reduced Dolosigranulum abundance. The stringent COVID-19 lockdown in Spain had a significant impact on the nasopharyngeal microbiota of children, reflected in the limited abundance of common respiratory pathobionts and the predominance of Corynebacterium, regardless of SARS-CoV-2 detection. COVID-19 severity in adults was associated with decreased nasopharynx levels of healthy commensal bacteria.

Concentrations of nitrogen compounds are related to severe rhinovirus infection in infants. A time-series analysis from the reference area of a pediatric university hospital in Barcelona.

BACKGROUND: There is scarce information focused on the effect of weather conditions and air pollution on specific acute viral respiratory infections, such as rhinovirus (RV), with a wide clinical spectrum of severity. OBJECTIVE: The aim of this study was to analyze the association between episodes of severe respiratory tract infection by RV and air pollutant concentrations (NOx and SO2 ) in the reference area of a pediatric university hospital. METHODS: An analysis of temporal series of daily values of NOx and SO2 , weather variables, circulating pollen and mold spores, and daily number of admissions in the pediatric intensive care unit (PICU) with severe respiratory RV infection (RVi) in children between 6 months and 18 years was performed. Lagged variables for 0-5 days were considered. The study spanned from 2010 to 2018. Patients with comorbidities were excluded. RESULTS: One hundred and fifty patients were admitted to the PICU. Median age was 19 months old (interquartile range [IQR]: 11-47). No relationship between RV-PICU admissions and temperature, relative humidity, cumulative rainfall, or wind speed was found. Several logistic regression models with one pollutant and two pollutants were constructed but the best model was that which included average daily NOx concentrations. Average daily NOx concentrations were related with the presence of PICU admissions 3 days later (odds ratio per IQR-unit increase: 1.64, 95% confidence interval: 1.20-2.25)). CONCLUSIONS: This study has shown a positive correlation between NOx concentrations at Lag 3 and children's PICU admissions with severe RV respiratory infection. Air pollutant data should be taken into consideration when we try to understand the severity of RVis.

New multivariable prediction model PEdiatric SEpsis recognition and stratification (PESERS score) shows excellent discriminatory capacity.

AIM: To develop a quantitative predictive scoring model for the early recognition and assessment of paediatric sepsis. METHODS: Prospective observational study including emergency department and in-hospital febrile patients under 18 years. Sepsis diagnose (Goldstein 2005 definitions) was the main outcome. Variables associated with the outcome were included in a multivariable analysis. Cut-off points, odds ratio and coefficients for the variables kept after the multivariable analysis were identified. The score was obtained from the coefficients, The AUC was obtained from ROC-analysis, and internal validation was performed using k-fold cross-validation. RESULTS: The analysis included 210 patients. 45 variables were evaluated and the bivariate analysis identified 24 variables associated with the outcome. After the multivariable regression, 11 variables were kept and the score was obtained. The model yielded an excellent AUC of 0.886 (95% CI 0.845-0.927), p < 0.001 for sepsis recognition. With a cut-off value of 5 for the score, we obtained a sensitivity of 98%, specificity of 76.7%, positive predictive value of 87.9% and negative predictive value of 93.3%. CONCLUSION: The proposed scoring model for paediatric sepsis showed adequate discriminatory capacity and sufficient accuracy, which is of great clinical significance in detecting sepsis early and predicting its severity. Nevertheless external validation is needed before clinical use.

Clinical impact of rapid viral respiratory panel testing on pediatric critical care of patients with acute lower respiratory infection.

BACKGROUND: We aimed to determine the impact of utilizing a rapid panel test of respiratory viral and atypical bacteria (FilmArray® Respiratory Panel, FA RP) on etiological diagnosis of acute lower respiratory infection (ALRI) and antimicrobial stewardship in critical care pediatric patients. METHODS: Prospective cohort study of patients aged<18 years with clinical diagnosis of ALRI that were admitted to the Pediatric Intensive Care Unit (PICU) of Hospital Sant Joan de Deu (Barcelona, Spain) during December 2015-February 2017. Patients were diagnosed by FA RP and by a bundle of routine microbiological assays. RESULTS: ALRI viral and bacterial etiology was confirmed by a composite reference standard of routine microbiological assays in 72 (55.4%) and 15 (11.5%) respiratory samples, respectively, that were collected from 130 children (median age, 3.5 months, IQR 1.1-14.8 months; 54.6% male). Comparatively, FA RP use increased etiological confirmation of ALRI in up to 123 (94.6%) samples (p<0.001) but only determined a bacterial origin in 2 (1.5%). Availability of diagnostic results before patient discharge from the PICU rose from 65.4 to 38.5% (p<0.001). Use of the new panel test directly influenced antimicrobial stewardship in 11 (8.4%) episodes, leading to discontinuation of antiviral drugs (n=5), administration of targeted antibiotics (n=3), antiviral therapy start (n=2) and both targeted antibiotic administration and discontinuation of antiviral drugs (n=1). CONCLUSION: FA RP contributed to improve etiological diagnosis of ALRI in a timely manner while enhancing a more rational use of antimicrobial drugs in critical care pediatric patients.

Clinical impact of rapid viral respiratory panel testing on pediatric critical care of patients with acute lower respiratory infection / Impacto clínico de una prueba rápida de detección múltiple de virus respiratorios en pacientes pediátricos críticos con infección respiratoria aguda de vías bajas

BackgroundWe aimed to determine the impact of utilizing a rapid panel test of respiratory viral and atypical bacteria (FilmArray® Respiratory Panel, FA RP) on etiological diagnosis of acute lower respiratory infection (ALRI) and antimicrobial stewardship in critical care pediatric patients.MethodsProspective cohort study of patients aged<18 years with clinical diagnosis of ALRI that were admitted to the Pediatric Intensive Care Unit (PICU) of Hospital Sant Joan de Deu (Barcelona, Spain) during December 2015–February 2017. Patients were diagnosed by FA RP and by a bundle of routine microbiological assays.ResultsALRI viral and bacterial etiology was confirmed by a composite reference standard of routine microbiological assays in 72 (55.4%) and 15 (11.5%) respiratory samples, respectively, that were collected from 130 children (median age, 3.5 months, IQR 1.1–14.8 months; 54.6% male). Comparatively, FA RP use increased etiological confirmation of ALRI in up to 123 (94.6%) samples (p<0.001) but only determined a bacterial origin in 2 (1.5%). Availability of diagnostic results before patient discharge from the PICU rose from 65.4 to 38.5% (p<0.001). Use of the new panel test directly influenced antimicrobial stewardship in 11 (8.4%) episodes, leading to discontinuation of antiviral drugs (n=5), administration of targeted antibiotics (n=3), antiviral therapy start (n=2) and both targeted antibiotic administration and discontinuation of antiviral drugs (n=1).ConclusionFA RP contributed to improve etiological diagnosis of ALRI in a timely manner while enhancing a more rational use of antimicrobial drugs in critical care pediatric patients.

AntecedentesNuestro objetivo fue determinar el impacto de la utilización de una prueba rápida de detección múltiple de virus y bacterias atípicas respiratorias (FilmArray® Respiratory Panel [FA RP]) en el diagnóstico etiológico de la infección respiratoria aguda de vías bajas (IRAVB) y en la administración de antimicrobianos en pacientes críticos pediátricos.MétodosEstudio de una cohorte prospectiva de pacientes <18 años con diagnóstico clínico de IRAVB que ingresaron en la Unidad de Cuidados Intensivos Pediátricos (UCIP) del Hospital Sant Joan de Deu, Barcelona, España, durante diciembre de 2015-febrero de 2017. Los pacientes fueron diagnosticados por FA RP y por un grupo de pruebas microbiológicas de rutina.ResultadosLas pruebas microbiológicas de rutina confirmaron la etiología viral y bacteriana de la IRAVB en 72 (55,4%) y 15 (11,5%) muestras respiratorias, respectivamente, obtenidas de 130 niños (edad mediana: 3,5 meses; rango intercuartil: 1,1-14,8 meses; 54,6% varones). Comparativamente, el uso de FA RP aumentó la confirmación etiológica de la IRAVB en hasta 123 (94,6%) muestras (p<0,001), pero solo determinó un origen bacteriano en 2 (1,5%). La disponibilidad de resultados diagnósticos antes del alta del paciente de la UCIP aumentó del 38,5 al 65,4% (p<0,001). El uso de la nueva prueba de detección múltiple influyó directamente en la administración de antimicrobianos en 11 (8,4%) episodios, orientando la interrupción de tratamientos antivirales (n=5), la administración de antibióticos dirigidos (n=3), el inicio de terapias antivirales (n=2) y la administración dirigida de antibióticos e interrupción simultánea de tratamiento antiviral (n=1).

Bronchiolitis, epidemiological changes during the SARS-CoV-2 pandemic.

BACKGROUND: Bronchiolitis is the most common viral infection of the lower respiratory tract in infants under 2 years of age. The aim of this study was to analyze and compare the seasonal bronchiolitis peaks before and during the SARS-CoV-2 pandemic. METHODS: Descriptive, prospective, and observational study. Patients with severe bronchiolitis admitted to the Pediatric Intensive Care Unit (PICU) of a referral tertiary hospital between September 2010 and June 2021 were included. Demographic data were collected. Viral laboratory-confirmation was carried out. Each season was analyzed and compared. The daily average temperature was collected. RESULTS: 1116 patients were recruited, 58.2% of them males. The median age was 49 days. Respiratory syncytial virus (RSV) was isolated in 782 cases (70.1%). In April 2021, the first and only case of bronchiolitis caused by SARS-CoV-2 was identified. The pre- and post-pandemic periods were compared. There were statistically significant differences regarding: age, 47 vs. 73 days (p = 0.006), PICU and hospital length of stay (p = 0.024 and p = 0.001, respectively), and etiology (p = 0.031). The peak for bronchiolitis in 2020 was non-existent before week 52. A delayed peak was seen around week 26/2021. The mean temperature during the epidemic peak was 10ºC for the years of the last decade and is 23ºC for the present season. CONCLUSION: The COVID-19 pandemic outbreak has led to a clearly observable epidemiological change regarding acute bronchiolitis, which should be studied in detail. The influence of the environmental temperature does not seem to determine the viral circulation.

Rapid Increase of Oral Bacteria in Nasopharyngeal Microbiota After Antibiotic Treatment in Children With Invasive Pneumococcal Disease.

Introduction: Antibiotics are commonly prescribed to young children for treating bacterial infections such as invasive pneumococcal disease (IPD) caused by Streptococcus pneumoniae. Despite the obvious benefits of antibiotics, little is known about their possible side effects on children's nasopharyngeal microbiota. In other ecological niches, antibiotics have been described to perturb the balanced microbiota with short- and long-term effects on children's health. The present study aims to evaluate and compare the nasopharyngeal microbiota of children with IPD and different degree of antibiotic exposure. Methods: We investigated differences in nasopharyngeal microbiota of two groups of children <18 years with IPD: children not exposed to antibiotics before sample collection (n=27) compared to children previously exposed (n=54). Epidemiological/clinical data were collected from subjects, and microbiota was characterized by Illumina sequencing of V3-V4 amplicons of the 16S rRNA gene. Results: Main epidemiological/clinical factors were similar across groups. Antibiotic-exposed patients were treated during a median of 4 days (IQR: 3-6) with at least one beta-lactam (100.0%). Higher bacterial richness and diversity were found in the group exposed to antibiotics. Different streptococcal amplicon sequence variants (ASVs) were differentially abundant across groups: antibiotic use was associated to lower relative abundances of Streptococcus ASV2 and Streptococcus ASV11 (phylogenetically close to S. pneumoniae), and higher relative abundances of Streptococcus ASV3 and Streptococcus ASV12 (phylogenetically close to viridans group streptococci). ASVs assigned to typical bacteria from the oral cavity, including Veillonella, Alloprevotella, Porphyromonas, Granulicatella, or Capnocytophaga, were associated to the antibiotic-exposed group. Common nosocomial genera such as Staphylococcus, Acinetobacter, and Pseudomonas were also enriched in the group exposed to antibiotics. Conclusion: Our results point toward a reduction of S. pneumoniae abundance on the nasopharynx of children with IPD after antibiotic treatment and a short-term repopulation of this altered niche by oral and nosocomial bacteria. Future research studies will have to evaluate the clinical implications of these findings and if these populations would benefit from the probiotic/prebiotic administration or even from the improvement on oral hygiene practices frequently neglected among hospitalized children.

Exploring the nasopharyngeal microbiota composition in infants with whooping cough: A test-negative case-control study.

PURPOSE: The purpose of this study was to characterize the nasopharyngeal microbiota of infants with possible and confirmed pertussis compared to healthy controls. METHODS: This prospective study included all infants <1 year with microbiologically confirmed diagnosis of pertussis attended at a University Hospital over a 12-month period. For each confirmed case, up to 2 consecutive patients within the same age range and meeting the clinical case definition of pertussis but testing PCR-negative were included as possible cases. A third group of asymptomatic infants (healthy controls) were also included. Nasopharyngeal microbiota was characterized by sequencing the V3-V4 region of the 16S rRNA gene. Common respiratory DNA/RNA viral co-infection was tested by multiplex PCR. RESULTS: Twelve confirmed cases, 21 possible cases and 9 healthy controls were included. Confirmed whooping cough was primarily driven by detection of Bordetella with no other major changes on nasopharyngeal microbiota. Possible cases had limited abundance or absence of Bordetella and a distinctive microbiota with lower bacterial richness and diversity and higher rates of viral co-infection than both confirmed cases and healthy controls. Bordetella reads determined by 16S rRNA gene sequencing were found in all 12 confirmed cases (100%), 3 out of the 21 possible cases (14.3%) but in any healthy control. CONCLUSION: This study supports the usefulness of 16S rRNA gene sequencing for improved sensitivity on pertussis diagnosis compared to real-time PCR and to understand other microbial changes occurring in the nasopharynx in children <1 year old with suspected whooping cough compared to healthy controls.

Lower Respiratory Tract Infection and Genus Enterovirus in Children Requiring Intensive Care: Clinical Manifestations and Impact of Viral Co-Infections.

Infection by rhinovirus (RV) and enterovirus (EV) in children ranges from asymptomatic infection to severe lower respiratory tract infection (LRTI). This cohort study evaluates the clinical impact of RV/EV species, alone or in codetection with other viruses, in young children with severe LRTI. Seventy-one patients aged less than 5 years and admitted to the Paediatric Intensive Care Unit (PICU) of a reference children's hospital with RV or EV (RV/EV) LRTI were prospectively included from 1/2018 to 3/2020. A commercial PCR assay for multiple respiratory pathogens was performed in respiratory specimens. In 22/71, RV/EV + respiratory syncytial virus (RSV) was found, and 18/71 had RV/EV + multiple viral detections. Patients with single RV/EV detection required invasive mechanical ventilation (IMV) as frequently as those with RSV codetection, whereas none of those with multiple viral codetections required IMV. Species were determined in 60 samples, 58 being RV. No EV-A, EV-C, or EV-D68 were detected. RV-B and EV-B were only found in patients with other respiratory virus codetections. There were not any associations between RV/EV species and severity outcomes. To conclude, RV/EV detection alone was observed in young children with severe disease, while multiple viral codetections may result in reduced clinical severity. Differences in pathogenicity between RV and EV species could not be drawn.

The Positive Rhinovirus/Enterovirus Detection and SARS-CoV-2 Persistence beyond the Acute Infection Phase: An Intra-Household Surveillance Study.

We aimed to assess the duration of nasopharyngeal severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA persistence in adults self-confined at home after acute infection; and to identify the associations of SARS-CoV-2 persistence with respiratory virus co-detection and infection transmission. A cross-sectional intra-household study was conducted in metropolitan Barcelona (Spain) during the time period of April to June 2020. Every adult who was the first family member reported as SARS-CoV-2-positive by reverse transcription polymerase chain reaction (RT-PCR) as well as their household child contacts had nasopharyngeal swabs tested by a targeted SARS-CoV-2 RT-PCR and a multiplex viral respiratory panel after a 15 day minimum time lag. Four-hundred and four households (404 adults and 708 children) were enrolled. SARS-CoV-2 RNA was detected in 137 (33.9%) adults and 84 (11.9%) children. Rhinovirus/Enterovirus (RV/EV) was commonly found (83.3%) in co-infection with SARS-CoV-2 in adults. The mean duration of SARS-CoV-2 RNA presence in adults' nasopharynx was 52 days (range 26-83 days). The persistence of SARS-CoV-2 was significantly associated with RV/EV co-infection (adjusted odds ratio (aOR) 9.31; 95% CI 2.57-33.80) and SARS-CoV-2 detection in child contacts (aOR 2.08; 95% CI 1.24-3.51). Prolonged nasopharyngeal SARS-CoV-2 RNA persistence beyond the acute infection phase was frequent in adults quarantined at home during the first epidemic wave; which was associated with RV/EV co-infection and could enhance intra-household infection transmission.

Validation and implementation of a direct RT-qPCR method for rapid screening of SARS-CoV-2 infection by using non-invasive saliva samples.

OBJECTIVE: To validate and implement an optimized screening method for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA combining use of self-collected raw saliva samples, single-step heat-treated virus inactivation and RNA extraction, and direct RT-qPCR. METHODS: This was a three-phase study conducted in Barcelona (Spain) during June to October, 2020. The three phases were (1) analytical validation against standard RT-qPCR in saliva samples; (2) diagnostic validation against standard RT-qPCR using paired saliva-nasopharyngeal samples obtained from asymptomatic teenagers and adults in a sports academy; and (3) pilot screening of asymptomatic health workers in a tertiary hospital. RESULTS: In phase 1, the detection yield of the new method was comparable to that of standard RT-qPCR. In phase 2, the diagnostic sensitivity and specificity values in 303 self-collected saliva samples were 95.7% (95% confidence interval 79.0-99.2%) and 100.0% (95% confidence interval 98.6-100.0%), respectively. In phase 3, only 17 (0.6%) of the saliva samples self-collected by 2709 participants without supervision were invalid. The rapid analytical workflow with the new method (up to 384 batched samples could be processed in less than 2 hours) yielded 24 (0.9%) positive results in the remaining 2692 saliva samples. Paired nasopharyngeal specimens were all positive by standard RT-qPCR. CONCLUSIONS: Direct RT-qPCR on self-collected raw saliva is a simple, rapid, and accurate method with potential to be scaled up for enhanced SARS-CoV-2 community-wide screening.