Evaluation of CLINITEST® Rapid Covid-19 + Influenza antigen test in a cohort of symptomatic patients in an emergency department.

OBJECTIVES: Rapid management of patients with respiratory tract infections in hospital emergency departments is one of the main objectives since the concurrent circulation of respiratory viruses following the SARS-CoV-2 pandemic. The use of new combined point-of-care antigen tests for detecting influenza A/B and SARS-CoV-2 represents an advantage in response time over the molecular tests. The objective was to evaluate the suitability of the CLINITEST® Rapid Covid-19 + Influenza Antigen test (Siemens Healthineers, Germany) (RCIA test) by measuring the sensitivity, specificity, Cohen's kappa, and cut-off values. METHODS: Nasopharyngeal samples were collected from a randomised group of symptomatic patients of all ages at emergency department during January-February 2023. In parallel, these patients were screened for influenza A/B, and SARS-CoV-2 using RT-PCR. The Ct (cycle threshold) values were collected for positive [RT-PCR (+) /RCIA test (+)] and false negative [(RT-PCR (+) /RCIA test (-)] samples. A subanalysis was performed in the paediatric population (< 16 years-old). RESULTS: We included 545 patients (55.8% females) with a median age of 7 years-old (IQR: 1-66.5). The RCIA test showed a sensitivity of 59.7% [95%CI: 46.9-67.33] for influenza A, 65.6% [95%CI: 49.5-80.3] for influenza B, and 76.9% [95%CI: 45.8-84.8] for SARS-CoV-2. The specificity was between 90.7%-99.7% with a moderate/high level of agreement with RT-PCR (kappa score: 0.6-0.8) for the three respiratory viruses included in the RCIA test. CONCLUSIONS: The sensitivity of the RCIA test is insufficient for screening of patients, including patients with low Ct values (Ct > 20). Despite its good specificity and Cohen's kappa value, its use as a screening test is not comparable to RT-PCR systems in the ED environment with a high number of false negative results.

Epidemiological changes in invasive Streptococcus pyogenes infection during the UK alert period: A molecular comparative analysis from a tertiary Spanish hospital in 2023.

OBJECTIVES: To study the genomic epidemiology of Streptococcus pyogenes causing bloodstream infections (GAS-BSI) in a Spanish tertiary hospital during the United Kingdom invasive S. pyogenes outbreak alert. METHODS: Retrospective epidemiological analysis of GAS-BSI during the January-May 2017-2023 period. WGS was performed using Ion torrent GeneStudio™ S5 system for emm typing and identification of superantigen genes in S. pyogenes isolated during the 2022-2023 UK outbreak alert. RESULTS: During 2023, there were more cases of GAS-BSI compared to the same period of previous year with a non-significant increase in children. Fourteen isolates were sequenced. The emm1 (6/14, 42.9%) and emm12 (2/14, 14.3%) types predominated; 5 of 6 (75%) emm1 isolates were from the M1UK clone. The most detected superantigen genes were speG (12/14, 85.7%), speC (10/14, 71.4%), speJ (7/14, 50%), and speA (5/15, 33.3%). speA and speJ were predominant in M1UK clone. CONCLUSIONS: Our genomic epidemiology in 2023 is similar to the reported data from the UK outbreak alert in the same period and different from previous national S. pyogenes surveillance reports.

Epidemiological changes in invasive Streptococcus pyogenes infection during the UK alert period: A molecular comparative analysis from a tertiary Spanish hospital in 2023

Objectives: To study the genomic epidemiology of Streptococcus pyogenes causing bloodstream infections (GAS-BSI) in a Spanish tertiary hospital during the United Kingdom invasive S. pyogenes outbreak alert. Methods: Retrospective epidemiological analysis of GAS-BSI during the January–May 2017–2023 period. WGS was performed using Ion torrent GeneStudio™ S5 system for emm typing and identification of superantigen genes in S. pyogenes isolated during the 2022–2023 UK outbreak alert. Results: During 2023, there were more cases of GAS-BSI compared to the same period of previous year with a non-significant increase in children. Fourteen isolates were sequenced. The emm1 (6/14, 42.9%) and emm12 (2/14, 14.3%) types predominated; 5 of 6 (75%) emm1 isolates were from the M1UK clone. The most detected superantigen genes were speG (12/14, 85.7%), speC (10/14, 71.4%), speJ (7/14, 50%), and speA (5/15, 33.3%). speA and speJ were predominant in M1UK clone. Conclusions: Our genomic epidemiology in 2023 is similar to the reported data from the UK outbreak alert in the same period and different from previous national S. pyogenes surveillance reports.(AU)

Objetivos: Estudiar la epidemiología genómica de aislados de Streptococcus pyogenes causantes de bacteriemia (GAS-BSI) en un hospital de tercer nivel español durante la alerta por incremento de infecciones invasivas por S. pyogenes en el Reino Unido. Métodos: Análisis epidemiológico retrospectivo de GAS-BSI durante el periodo enero-mayo 2017-2023. Se realizó una secuenciación de genoma completo con el sistema Ion torrent GeneStudio™ S5 de los aislados obtenidos durante la alerta de brote del Reino Unido 2022-2023 para tipificación emm e identificación de genes de superantígenos. Resultados: Durante el periodo enero-mayo de 2023 hubo más casos de GAS-BSI que en el mismo periodo de años anteriores con un aumento no significativo en niños. Se secuenciaron 14 aislados. Predominaron los tipos emm1 (6/14, 42,9%) y emm12 (2/14, 14,3%); 5 de 6 (75%) aislados emm1 eran del clon M1UK. Los genes de superantígenos más detectados fueron speG (12/14, 85,7%), speC (10/14, 71,4%), speJ (7/14, 50%) y speA (5/15, 33,3%). Los genes speA y speJ predominaron en el clon M1UK. Conclusiones: Nuestra epidemiología genómica de Streptococcus pyogenes causantes de bacteriemia en 2023 es similar a los datos comunicados por el Reino Unido durante el mismo periodo y diferente de los informes nacionales previos de vigilancia.(AU)

The CARBA-MAP study: national mapping of carbapenemases in Spain (2014-2018).

Introduction: Infections caused by carbapenem-resistant Enterobacterales (CRE) and carbapenem-resistant Pseudomonas aeruginosa, including isolates producing acquired carbapenemases, constitute a prevalent health problem worldwide. The primary objective of this study was to determine the distribution of the different carbapenemases among carbapenemase-producing Enterobacterales (CPE, specifically Escherichia coli, Klebsiella pneumoniae, Enterobacter cloacae complex, and Klebsiella aerogenes) and carbapenemase-producing P. aeruginosa (CPPA) in Spain from January 2014 to December 2018. Methods: A national, retrospective, cross-sectional multicenter study was performed. The study included the first isolate per patient and year obtained from clinical samples and obtained for diagnosis of infection in hospitalized patients. A structured questionnaire was completed by the participating centers using the REDCap platform, and results were analyzed using IBM SPSS Statistics 29.0.0. Results: A total of 2,704 carbapenemase-producing microorganisms were included, for which the type of carbapenemase was determined in 2692 cases: 2280 CPE (84.7%) and 412 CPPA (15.3%), most often using molecular methods and immunochromatographic assays. Globally, the most frequent types of carbapenemase in Enterobacterales and P. aeruginosa were OXA-48-like, alone or in combination with other enzymes (1,523 cases, 66.8%) and VIM (365 cases, 88.6%), respectively. Among Enterobacterales, carbapenemase-producing K. pneumoniae was reported in 1821 cases (79.9%), followed by E. cloacae complex in 334 cases (14.6%). In Enterobacterales, KPC is mainly present in the South and South-East regions of Spain and OXA-48-like in the rest of the country. Regarding P. aeruginosa, VIM is widely distributed all over the country. Globally, an increasing percentage of OXA-48-like enzymes was observed from 2014 to 2017. KPC enzymes were more frequent in 2017-2018 compared to 2014-2016. Discussion: Data from this study help to understand the situation and evolution of the main species of CPE and CPPA in Spain, with practical implications for control and optimal treatment of infections caused by these multi-drug resistant organisms.

Are cerebrospinal fluid biochemical parameters valid to predict positive results in microbiological molecular diagnostic platforms? A 4-year experience with the FilmArray® Panel Meningitis/Encephalitis for detection of community-acquired bacterial meningitis.

OBJECTIVE: To demonstrate whether the use of the FilmArray® Meningitis/Encephalitis panel (M/E) in the diagnosis of bacterial meningitis can be optimized based on the screening of cerebrospinal fluid biochemical parameters and whether there is a correlation between biochemical data and positive results of the technique. MATERIAL AND METHODS: We used data from La Paz University Hospital between September 5, 2017 and December 1, 2021, from patients who had had the FilmArray® panel M/E performed on cerebrospinal fluid samples. RESULTS: Bacterial meningitis was suspected in 63.9% of the patients; 38.15% had a positive result on the FilmArray® panel M/E, of which 68.97% were isolated in culture. Of the biochemical parameters studied in cerebrospinal fluid, white blood cell count, lactate, and protein were increased in PCR-positive patients, but glucose was decreased. DISCUSSION: Only lactate showed a significant contribution to the model, with a cut-off point of 4.65 mmol/L with a sensitivity of 81.5% and a specificity of 96.4%.

Staphylococcus aureus bacteremia in patients with SARS-CoV-2 infection.

Objectives: The aim was to compare the incidence of Staphylococcus aureus bacteremia in COVID-19 and non-COVID-19 adult patients during the pandemic period versus the previous two years. Also, we described the characteristics of both cohorts of patients in pandemic period to find differences. Material and methods: Retrospective study in our tertiary-care centre reviewing S. aureus bacteremia episodes in COVID-19 and non-COVID-19 patients through clinical records and the Microbiology Department database. Results: In 2018 and 2019, the incidence of S. aureus bacteremia episodes was 1.95 and 1.63 per 1000 admissions respectively. In the pandemic period, global incidence was 1.96 episodes per 1000 non-COVID-19 admissions and 10.59 episodes per 1000 COVID-19 admissions. A total of 241 bacteremia was registered during this pandemic period in 74 COVID-19 patients and in 167 non-COVID-19 patients. Methicillin resistance was detected in 32.4% and 13.8% of isolates from COVID-19 and non-COVID-19 patients respectively. In COVID-19 patients, mortality rates were significantly higher. Conclusions: We showed a significantly high rates of S. aureus bacteremia incidence in COVID-19 patients and higher methicillin resistance and 15-day mortality rates than in non-COVID-19 patients.

Objetivos: Comparar la incidencia de bacteriemias por Staphylococcus aureus en pacientes adultos COVID-19 y no-COVID-19 durante la pandemia frente a los 2 años previos. Además, describimos las características de ambas cohortes en periodo pandémico para encontrar diferencias. Material y métodos: Estudio retrospectivo en nuestro centro de tercer nivel a través de historias clínicas y la base de datos del Servicio de Microbiología. Resultados: En 2018 y 2019, la incidencia de bacteriemias fue de 1.95 y 1,63 casos por cada 1.000 ingresos respectivamente. En pandemia, la incidencia global fue de 1,96 casos por cada 1.000 ingresos no-COVID-19 y de 10,59 casos por cada 1.000 ingresos COVID-19. Durante la pandemia se registraron 241 bacteriemias en 74 pacientes COVID-19 y en 167 pacientes no-COVID-19. La resistencia a meticilina se detectó en el 32,4 y 13,8% de los aislados de pacientes COVID-19 y no-COVID-19 respectivamente. En pacientes COVID-19 la mortalidad fue significativamente mayor. Conclusiones: Mostramos una incidencia significativamente alta de bacteriemias por S. aureus en pacientes COVID-19, así como mayores tasas de resistencia a meticilina y mortalidad a los 15 días que en pacientes no-COVID-19.

Staphylococcus aureus bacteremia in patients with SARS-CoV-2 infection.

OBJECTIVES: The aim was to compare the incidence of Staphylococcus aureus bacteremia in COVID-19 and non-COVID-19 adult patients during the pandemic period versus the previous two years. Also, we described the characteristics of both cohorts of patients in pandemic period to find differences. MATERIAL AND METHODS: Retrospective study in our tertiary-care centre reviewing S. aureus bacteremia episodes in COVID-19 and non-COVID-19 patients through clinical records and the Microbiology Department database. RESULTS: In 2018 and 2019, the incidence of S. aureus bacteremia episodes was 1.95 and 1.63 per 1000 admissions respectively. In the pandemic period, global incidence was 1.96 episodes per 1000 non-COVID-19 admissions and 10.59 episodes per 1000 COVID-19 admissions. A total of 241 bacteremia was registered during this pandemic period in 74 COVID-19 patients and in 167 non-COVID-19 patients. Methicillin resistance was detected in 32.4% and 13.8% of isolates from COVID-19 and non-COVID-19 patients respectively. In COVID-19 patients, mortality rates were significantly higher. CONCLUSIONS: We showed a significantly high rates of S. aureus bacteremia incidence in COVID-19 patients and higher methicillin resistance and 15-day mortality rates than in non-COVID-19 patients.

Pertactin-Deficient Bordetella pertussis with Unusual Mechanism of Pertactin Disruption, Spain, 1986-2018.

Bordetella pertussis not expressing pertactin has increased in countries using acellular pertussis vaccines (ACV). The deficiency is mostly caused by pertactin gene disruption by IS481. To assess the effect of the transition from whole-cell vaccine to ACV on the emergence of B. pertussis not expressing pertactin in Spain, we studied 342 isolates collected during 1986-2018. We identified 93 pertactin-deficient isolates. All were detected after introduction of ACV and represented 38% of isolates collected during the ACV period; 58.1% belonged to a genetic cluster of isolates carrying the unusual prn::del(-292, 1340) mutation. Pertactin inactivation by IS481 insertion was identified in 23.7% of pertactin-deficient isolates, arising independently multiple times and in different phylogenetic branches. Our findings support the emergence and dissemination of a cluster of B. pertussis with an infrequent mechanism of pertactin disruption in Spain, probably resulting from introduction of ACV.

Molecular diagnosis of bacteremia in a pediatric intensive care unit: a step forward.

Aim: T2Bacteria® Panel detects six ESKAPE pathogens in around 3.5 h directly in whole blood. Our aim was to compare T2Bacteria with simultaneous blood culture in critically ill children with suspected bloodstream infection. Materials & methods: Retrospective study of critically ill children admitted to our tertiary-care center (2018-2020). Results: A total of 60 patients were recruited, including 63 episodes and 75 T2Bacteria/blood cultures were performed. Overall agreement between T2Bacteria and blood culture was 78.7% with a discordance of 21.3% (16/75 samples). Conclusion: T2Bacteria Panel may be useful in critically ill children providing an accurate and fast diagnosis of bacteremia directly from blood sample and detecting pathogens not recovered in blood cultures.

Microbial Identification in the Clinical Microbiology Laboratory Using MALDI-TOF-MS.

MALDI-TOF mass spectrometry has been applied with huge success to the identification of cultured microorganisms in clinical microbiology laboratories where it has become the reference method because it is simple, fast, and highly reproducible. We describe the different procedures used in the routine for pathogen identification using the Bruker MALDI Biotyper® system.

PCR urgente de Bordetella en lactantes menores de 3 meses, una herramienta útil en el Servicio de Urgencias Pediátricas / Urgent Bordetella PCR in infants under 3 months, a useful tool in the Pediatric Emergency Department

Introducción: En pacientes menores de 3 meses con sospecha de tosferina se recomienda ingreso y tratamiento con azitromicina debido a su mayor morbimortalidad, por lo que muchos pacientes con tos sin otros signos de alarma ingresan con antibioterapia hasta obtener el resultado de la PCR de Bordetella. La realización de esta técnica de forma urgente proporciona el diagnóstico en pocas horas. Nuestro objetivo fue determinar si su introducción en los servicios de Urgencias mejoraba el manejo de estos pacientes. Métodos: Estudio de cohortes histórico de pacientes menores de 3 meses a los que se realizó en Urgencias la PCR de Bordetella de secreciones respiratorias desde marzo de 2011 hasta diciembre de 2017. A partir de diciembre de 2015 era procesada de forma urgente. Resultados: Se realizaron 158 PCR, 16 (10%) de las cuales resultaron positivas para B. pertussis. Los resultados negativos (142; 90%) se dividen en 2 grupos de estudio: PCR-convencional, con 74 casos, y PCR-urgente, con 68 casos. Los 2 grupos son homogéneos en cuanto a características clínicas y analíticas. En el grupo PCR-urgente se realizaron un 18% menos de radiografías de tórax (p=0,008) e ingresaron 33 pacientes (48,5%), frente a 49 (66,2%) en el grupo PCR-convencional (p=0,042). Recibió tratamiento antibiótico el 32% en el grupo PCR-urgente frente al 67% en el PCR-convencional (p=0,000047), sin aumento significativo de las reconsultas en Urgencias ni peor evolución. Conclusiones: La PCR urgente de Bordetella es una herramienta útil en los servicios de Urgencias para el manejo de los lactantes menores de 3 meses con sospecha de tosferina, ya que puede evitar ingresos, pruebas y tratamientos antibióticos innecesarios.(AU)

Introduction: Whooping cough in patients aged under 3 months has higher rates of morbimortality. Hospitalization and treatment with azithromycin is generally recommended. Many patients with cough without other signs of alarm, are admitted and started antibiotic therapy until a result of Bordetella-PCR is available. This technique, when performed urgently, can provide the diagnosis in a few hours. The objective of this study is to determine if its generalisation in the Emergency Department allows to improve patient management. Methods: Retrospective cohort study of patients aged under 3 months who underwent Bordetella-PCR testing from upper respiratory tract secretions since March 2011 to December 2017. From December 2015 the test was performed urgently. Results: One hundred and fifty-eight PCR were performed, 16 (10%) were positive for B. pertussis. Negative results (142; 90%) were divided in 2 cohorts: conventional-PCR, with 74 cases, and urgent-PCR, with 68 cases. The 2 groups were homogeneous in terms of clinical and analytical characteristics. In the urgent-PCR group there was 18% reduction in chest X-rays performed (P=.008). There were 33 (48.5%) patients admitted in the urgent-PCR group, compared to 49 (66.2%) in the conventional-PCR (P=.042). Antibiotic treatment was initiated in 32% of the patients in the urgent-PCR group compared to 67% in the conventional-PCR group (P=.000047), without observing any significant increase in the number of visits to the Emergency Department or worse clinical performance. Conclusions: The introduction of urgent PCR in the Emergency Department is a useful tool in the management of infants under 3 months of age with suspected pertussis, since it can avoid unnecessary admissions, diagnostic tests and antibiotic treatments.(AU)

Think of the Children: Evaluation of SARS-CoV-2 Rapid Antigen Test in Pediatric Population.

BACKGROUND: Real-time reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is the reference laboratory method to diagnose SARS-CoV-2 infection then requires equipment and is time-consuming. There is a crucial demand for rapid techniques such as antigen detection test. Considering the different diagnostic accuracy of tests with other respiratory viruses in adults and children, SARS-CoV-2 antigen test must be evaluated specifically in children. METHODS: The purpose of this study was to evaluate the performance of Panbio COVID-19 Ag Rapid Test Device (Abbott) as a point-of-care test for diagnosis of SARS-CoV-2 in comparison to RT-qPCR in a pediatric population. RESULTS: Four hundred forty nasopharyngeal swabs were tested. Amongst the 18 positive RT-qPCR samples, 14 were detected by the rapid antigen test, given an overall sensitivity of 77.7%. All the samples detected positive with the antigen rapid test were also positive with RT-qPCR. CONCLUSION: The sensitivity of Panbio COVID-19 Ag Rapid Test Device is lower in children than in adults. Nevertheless, considering the good values of specificity, negative and positive predictive values this test could be used as a frontline test to obtain quick results, although the negative values with COVID-19 high clinical suspicion should be confirmed using RT-qPCR.

Urgent Bordetella PCR in infants under 3 months, a useful tool in the Pediatric Emergency Department. / PCR urgente de Bordetella en lactantes menores de 3 meses, una herramienta útil en el Servicio de Urgencias Pediátricas.

INTRODUCTION: Whooping cough in patients aged under 3 months has higher rates of morbimortality. Hospitalization and treatment with azithromycin is generally recommended. Many patients with cough without other signs of alarm, are admitted and started antibiotic therapy until a result of Bordetella-PCR is available. This technique, when performed urgently, can provide the diagnosis in a few hours. The objective of this study is to determine if its generalisation in the Emergency Department allows to improve patient management. METHODS: Retrospective cohort study of patients aged under 3 months who underwent Bordetella-PCR testing from upper respiratory tract secretions since March 2011 to December 2017. From December 2015 the test was performed urgently. RESULTS: One hundred and fifty-eight PCR were performed, 16 (10%) were positive for B. pertussis. Negative results (142; 90%) were divided in 2 cohorts: conventional-PCR, with 74 cases, and urgent-PCR, with 68 cases. The 2 groups were homogeneous in terms of clinical and analytical characteristics. In the urgent-PCR group there was 18% reduction in chest X-rays performed (P=.008). There were 33 (48.5%) patients admitted in the urgent-PCR group, compared to 49 (66.2%) in the conventional-PCR (P=.042). Antibiotic treatment was initiated in 32% of the patients in the urgent-PCR group compared to 67% in the conventional-PCR group (P=.000047), without observing any significant increase in the number of visits to the Emergency Department or worse clinical performance. CONCLUSIONS: The introduction of urgent PCR in the Emergency Department is a useful tool in the management of infants under 3 months of age with suspected pertussis, since it can avoid unnecessary admissions, diagnostic tests and antibiotic treatments.

Evaluation of three immunochromatographic tests for rapid detection of antibodies against SARS-CoV-2.

Lateral flow immunoassays (LFIA) for rapid detection of specific antibodies (IgM and IgG) against SARS-CoV-2 in different human specimens have been developed in response to the pandemic. The aim of this study is to evaluate three immunocromathographic assays (Sienna®, Wondfo® and Prometheus®) for detection of antibodies against SARS-CoV-2 in serum samples, considering RT-qPCR as a reference. A total of 145 serum samples from 145 patients with clinical suspicion of COVID-19 were collected: all of the samples were tested with Sienna®, 117 with Wondfo® and 89 with Prometheus®. The overall results of sensitivity, specificity, positive predictive value and negative predictive value obtained were as follows: 64.4%, 75%, 85.5% and 47.8% with Sienna®; 45.2%, 81.8%, 80.5% and 47.4% with Wondfo® and 75.5%, 12.5%, 51.4% and 29.4% with Prometheus®. The accuracy of the test for Sienna®, Wondfo® and Prometheus® was 67.6%, 59% and 47.2%, with a prevalence of COVID-19 of 69.7%, 62.4% and 55.1% respectively. Sensitivity of the three tests (Sienna®, Wondfo® and Prometheus® respectively) along the three different stages was 36.6%, 18.8% and 68.6% in the early stage (first week); 81.3%, 74.1% and 90.9% in the intermediate stage (second week) and 100%, 83.3% and 100% in the late stage (third week). The results demonstrate that even though Prometheus® presented a high sensitivity, the specificity was notably lower than the other two tests. Sienna® showed the greatest contrast between sensitivity and specificity, achieving the best accuracy, followed by Wondfo®. The sensitivity of the three ICT assays was higher in late stages of the disease.