Reliable resolution of ambiguous hepatitis C virus genotype 1 results with the Abbott HCV Genotype Plus RUO assay

Accurate subtyping of hepatitis C virus genotype 1 (HCV-1) remains clinically and epidemiologically relevant. The Abbott HCV Genotype Plus RUO (GT Plus) assay, targeting the core region, was evaluated as a reflex test to resolve ambiguous HCV-1 results in a challenging sample collection. 198 HCV-1 specimens were analysed with GT Plus (38 specimens with and 160 without subtype assigned by the Abbott RealTime Genotype II (GT II) assay targeting the 5'NC and NS5B regions). Sanger sequencing of the core and/or NS5B regions were performed in 127 specimens without subtype assignment by GT II, with "not detected" results by GT Plus, or with mixed genotypes/subtypes. The remaining GT Plus results were compared to LiPA 2.0 (n = 45) or just to GT II results if concordant (n = 26). GT Plus successfully assigned the subtype in 142/160 (88.8%) samples. "Not detected" results indicated other HCV-1 subtypes/genotypes or mismatches in the core region in subtype 1b. The subtyping concordance between GT Plus and either sequencing or LiPA was 98.6% (140/142). Therefore, combined use of GT II and GT Plus assays represents a reliable and simple approach which considerably reduced the number of ambiguous HCV-1 results and enabled a successful subtyping of 98.9% of all HCV-1 samples

Disseminated tuberculosis and diagnosis delay during the COVID-19 era in a Western European country : a case series analysis

Disseminated tuberculosis is frequently associated with delayed diagnosis and a poorer prognosis. To describe case series of disseminated TB and diagnosis delay in a low TB burden country during the COVID-19 period. We consecutively included all patients with of disseminated TB reported from 2019 to 2021 in the reference hospital of the Northern Crown of the Metropolitan Area of Barcelona. We collected socio-demographic information, clinical, laboratory and radiological findings. We included all 30 patients reported during the study period-5, 9, and 16 in 2019, 2020, and 2021 respectively-20 (66.7%) of whom were male and whose mean age was 41 years. Twenty-five (83.3%) were of non-EU origin. The most frequent system involvement was central nervous system (N = 8; 26.7%) followed by visceral (N = 7; 23.3%), gastro-intestinal (N = 6, 20.0%), musculoskeletal (N = 5; 16.7%), and pulmonary (N = 4; 13.3%). Hypoalbuminemia and anemia were highly prevalent (72 and 77%). The median of diagnostic delay was 6.5 months (IQR 1.8-30), which was higher among women (36.0 vs. 3.5 months; p = 0.002). Central nervous system involvement and pulmonary involvement were associated with diagnostic delay among women. We recorded 24 cured patients, two deaths, three patients with post-treatment sequelae, and one lost-to-follow up. We observed a clustering effect of patients in low-income neighborhoods (p < 0.001). There was a substantial delay in the diagnosis of disseminated TB in our study region, which might impacted the prognosis with women affected more negatively. Our results suggest that an increase in the occurrence of disseminated TB set in motion by diagnosis delay may have been a secondary effect of the COVID-19 pandemic

Corrigendum : Disseminated tuberculosis and diagnosis delay during the COVID-19 era in a Western European country: a case series analysis

Disseminated tuberculosis is frequently associated with delayed diagnosis and a poorer prognosis. To describe case series of disseminated TB and diagnosis delay in a low TB burden country during the COVID-19 period. We consecutively included all patients with of disseminated TB reported from 2019 to 2021 in the reference hospital of the Northern Crown of the Metropolitan Area of Barcelona. We collected socio-demographic information, clinical, laboratory and radiological findings. We included all 30 patients reported during the study period-5, 9, and 16 in 2019, 2020, and 2021 respectively-20 (66.7%) of whom were male and whose mean age was 41 years. Twenty-five (83.3%) were of non-EU origin. The most frequent system involvement was central nervous system (N = 8; 26.7%) followed by visceral (N = 7; 23.3%), gastro-intestinal (N = 6, 20.0%), musculoskeletal (N = 5; 16.7%), and pulmonary (N = 4; 13.3%). Hypoalbuminemia and anemia were highly prevalent (72 and 77%). The median of diagnostic delay was 6.5 months (IQR 1.8-30), which was higher among women (36.0 vs. 3.5 months; p = 0.002). Central nervous system involvement and pulmonary involvement were associated with diagnostic delay among women. We recorded 24 cured patients, two deaths, three patients with post-treatment sequelae, and one lost-to-follow up. We observed a clustering effect of patients in low-income neighborhoods (p < 0.001). There was a substantial delay in the diagnosis of disseminated TB in our study region, which might impacted the prognosis with women affected more negatively. Our results suggest that an increase in the occurrence of disseminated TB set in motion by diagnosis delay may have been a secondary effect of the COVID-19 pandemic

Mejora del diagnostico y caracterización molecular de la infección virémica de la hepatitis c en personas que se inyectan drogas

L'hepatitis C és una de les principals causes de cirrosi i carcinoma hepatocel·lular a nivell mundial. El 2015, l'Organització Mundial de la Salut (OMS) va elaborar un pla estratègic per a l'eliminació de les hepatitis víriques com a problema de salut pública el 2030. Per tal d'aconseguir-ho, és necessari dissenyar estratègies de prevenció, diagnòstic i tractament innovadores. Malgrat ser un dels principals focus d'hepatitis C, les taxes de diagnòstic i tractament en persones que s'injecten drogues (PQID) són molt baixes. L'estudi HepCdetect II es va centrar en la millora del diagnòstic i caracterització de l'epidèmia pel virus de l'hepatitis C (VHC) en PQID. El projecte es va dur a terme en 410 PQID en actiu i que acudien a serveis de reducció de danys a Catalunya, on els usuaris poden obtenir material d'injecció. Es va avaluar la detecció de la infecció virèmica (RNA-VHC) en mostres de sang seca obtinguda per punció dactilar (dried blood spots, DBS) com a estratègia de cribratge i confirmació del VHC alternativa a l'algoritme clàssic, que es basa en la detecció dels anticossos i, si positius, la detecció del RNA-VHC en plasma venós. Els DBS permetrien descentralitzar el diagnòstic i evitar la venopunció, entre d'altres avantatges. La tècnica basada en DBS va resultar molt sensible i especifica (97,2% i 100%, respectivament), i no es van observar diferencies significatives en el nombre d'individus amb infecció virèmica identificats en comparació amb l'algoritme clàssic en dos passos. També es va estudiar la diversitat genètica del virus tant inter- com intra-hoste (el VHC circula dins l'individu en forma de múltiples variants estretament relacionades entre sí) mitjançant seqüenciació massiva. Això va permetre diferenciar els individus amb una infecció aguda (dins els sis primers mesos de la infecció) de les infeccions cròniques amb una sensibilitat del 93,3% i una especificitat del 95,0%. El 13,5% dels participants amb hepatitis C varen ser identificats com infeccions agudes, el que va permetre determinar el perfil d'aquests participants. A la vegada, es va poder estimar la incidència del VHC, que oscil·lava entre 31 i 59/100 persones/any. Paral·lelament, es va dur a terme un anàlisi filogenètic a partir de les dades de seqüenciació, que va permetre identificar aquells individus involucrats en events de transmissió recents (el 46,8% de les PQID amb infecció virèmica), i descriure el seu perfil, el que permetrà dissenyar estratègies de prevenció i tractament més dirigides. Per últim, es va avaluar un assaig en el punt d'atenció (Xpert® HCV VL Fingerstick) que utilitza sang capil·lar fresca per a la detecció i quantificació del RNA-VHC en una hora en PQID en un dels centres de reducció de danys. Aquest assaig va mostrar una sensibilitat del 98,4% i una especificitat del 100% en comparació amb el mateix assaig en mostres aparellades de plasma venós. Les dues tècniques avaluades (DBS i Xpert® HCV VL Fingerstick) són ben acceptades per la població de PQID i faciliten la descentralització i simplificació del diagnòstic en una població amb baixa vinculació al sistema sanitari, amb el potencial d'ajudar a assolir els objectius d'eliminació establerts per la OMS.La hepatitis C es una de las principales causas de cirrosis y carcinoma hepatocelular a nivel mundial. En 2015, la Organización Mundial de la Salud (OMS) elaboró un plan estratégico para la eliminación de las hepatitis víricas como problema de salud pública en 2030. Para conseguirlo, es necesario diseñar estrategias de prevención, diagnóstico y tratamiento innovadoras. Pese a ser uno de los principales focos de hepatitis C, las tasas de diagnóstico y tratamiento en personas que se inyectan drogas (PQID) son muy bajas. El estudio HepCdetect II se centró en la mejora del diagnóstico y caracterización de la epidemia por el virus de la hepatitis C (VHC) en PQID. El proyecto se llevó a cabo en 410 PQID en activo y que acudían a servicios de reducción de daños en Cataluña, donde los usuarios pueden obtener material de inyección. Se evaluó la detección de la infección virémica (RNA-VHC) en muestras de sangre seca obtenida por punción dactilar (dried blood spots, DBS) como estrategia de cribado y confirmación del VHC alternativa al algoritmo clásico, que se basa en la detección de los anticuerpos y, si positivos, la detección del RNA-VHC en plasma venoso. Los DBS permitirían descentralizar el diagnóstico y evitar la venopunción, entre otras ventajas. La técnica basada en DBS resultó muy sensible y especifica (97,2% y 100%, respectivamente), no observándose diferencias significativas en el número de individuos con infección virémica identificados en comparación con el algoritmo clásico en dos pasos. También se estudió la diversidad genética del virus tanto inter- como intra-huésped (el VHC circula dentro del individuo en forma de múltiples variantes estrechamente relacionadas entre sí) mediante secuenciación masiva. Esto permitió diferenciar a los individuos con una infección aguda (dentro de los seis primeros meses de la infección) de las infecciones crónicas con una sensibilidad del 93,3% y una especificidad del 95,0%. El 13,5% de los participantes con hepatitis C fueron identificados como infecciones agudas, lo que permitió determinar el perfil de estos participantes. A su vez, se pudo estimar la incidencia del VHC, que oscilaba entre 31 y 59/100 personas/año. Paralelamente, se llevó a cabo un análisis filogenético a partir de los datos de secuenciación, que permitió identificar a aquellos individuos involucrados en eventos de transmisión recientes (el 46,8% de las PQID con infección virémica), así como describir su perfil, lo que permitirá diseñar estrategias de prevención y tratamiento más dirigidas. Por último, se evaluó un ensayo en el punto de atención (Xpert® HCV VL Fingerstick) que utiliza sangre capilar fresca para la detección del RNA-VHC en una hora en PQID en uno de los centros de reducción de daños. Este ensayo mostró una sensibilidad del 98,4% y una especificidad del 100% en comparación con el mismo ensayo en muestras pareadas de plasma venoso. Las dos técnicas evaluadas (DBS y Xpert® HCV VL Fingerstick) son bien aceptadas por la población de PQID y facilitan la descentralización y simplificación del diagnóstico en una población con baja vinculación al sistema sanitario, con el potencial de ayudar a alcanzar los objetivos de eliminación establecidos por la OMS.Hepatitis C is a leading cause of cirrhosis and hepatocellular carcinoma worldwide. In 2015, the World Health Organization (WHO) developed a strategic plan for the elimination of viral hepatitis as a public health problem by 2030. To achieve this, innovative prevention, diagnosis and treatment strategies need to be designed. Despite being a major hotspot for hepatitis C, diagnosis and treatment rates in people who inject drugs (PWID) are very low. The HepCdetect II study focused on improving the diagnosis and characterization of the hepatitis C virus (HCV) epidemic in PWID. The project was carried out in 410 active PWID attending harm reduction services in Catalonia, where users can obtain injection material. The detection of active infection (HCV-RNA) in dried blood spot (DBS) samples was evaluated as an alternative HCV screening and confirmation strategy to the classical algorithm, which is based on antibody detection and, if positive, RNA-HCV detection in plasma. DBS would allow for decentralization of diagnosis and avoidance of venipuncture, among other advantages. The DBS-based technique was very sensitive and specific (97.2% and 100%, respectively), with no significant differences in the number of individuals with active infection identified compared to the classical two-step algorithm. The genetic diversity of the virus was also studied both at inter- and intra-host level (HCV circulates within the individual as multiple closely related variants) by next-generation sequencing. This allowed us to differentiate individuals with acute infection (within the first six months of infection) from chronic infections with a sensitivity of 93.3% and a specificity of 95.0%. Among those participants with active hepatitis C infection, 13.5% were identified as acute infections, which made it possible to determine their profile. We also estimated the incidence of HCV, which ranged from 31 to 59/100 person-years. In parallel, a phylogenetic analysis was carried out from sequencing data, which made it possible to identify those individuals involved in recent transmission events (46.8% of those PWID with viremic infection), as well as their profile, which will allow to design targeted prevention and treatment strategies. Finally, a point-of-care assay (Xpert® HCV VL Fingerstick) using capillary blood was evaluated for 1-hour HCV-RNA detection in PWID at one of the harm reduction centers. This assay showed 98.4% sensitivity and 100% specificity in comparison with the same assay in paired venous plasma samples. The two assays evaluated (DBS and Xpert® HCV VL Fingerstick) are well accepted by the study population and facilitate the decentralization and simplification of diagnosis in a population with low linkage to the healthcare system, with the potential to help achieve the elimination targets set by the WHO.Universitat Autònoma de Barcelona. Programa de Doctorat en Microbiologi

Impact of the MALDI-TOF as a tool for bacterial identification in the frequency of isolation of Aerococcus spp and Actinotignum schaalii in urinary tract infection

Background: Actinotignum schaalii and the genus Aerococcus are considered emerging pathogens, since their isolation has been rising the last years thanks to the improvement of diagnosis techniques, such as the implementation of MALDI-TOF in microbiology laboratories for routine. Their patogenicity is nowadays well described in urinary tract infections affecting susceptible individuals, although both have been isolated from other biological samples. The aim of our study is to evaluate the impact of using mass spectrometry technology on the frequency of isolation of Aerococcus spp and A. schaalii in our hospital. Methods: From January 2014 and December 2015 44.654 urines were collected in our laboratory from patients that were expected to have an UTI. Samples were processed using a flow cytometer and cultured if applicable. After 48 h, microbial growth was assessed. Due to the suspicion of an Aerococcus spp or A. schaalii infection identification test was performed using Vitek2 until 2014 and MALDI-TOF from 2015. Results: Between the period of study, a total of 35 Aerococcus spp/A. schaalii isolates were collected from 34 patients. Six isolates were identified by Vitek2 and the other 29 were identified by MALDI-TOF. Out of 34 patients, 33 had at least one risk factor including age >65 years, immunosuppression or cancer, abnormality of the genitourinary tract, recurrent UTI, diabetes or a catheterization. Conclusions: Since the implementation of the MALDI-TOF in the laboratory the isolation of Aerococcus spp/A. schaalii has increased almost five times. The most frequent patient corresponds to an elderly patient with recurrent UTI and cancer. Resumen: Introducción: Actinotignum schaalii y el género Aerococcus son considerados patógenos emergentes debido al aumento en los últimos años de su aislamiento gracias a la mejora de las técnicas diagnósticas, como la implementación del MALDI-TOF en la rutina de los laboratorios de microbiología. Su patogenicidad está bien descrita en las infecciones del tracto urinario (ITU) en individuos susceptibles, aunque los dos géneros se han aislado también en otras muestras biológicas. El objetivo de nuestro estudio es evaluar el impacto del uso de la espectrometría de masas en la frecuencia de aislamiento de Aerococcus spp/A. schaalii en nuestro hospital. Métodos: Desde enero 2014 a diciembre 2015 se recibieron 44.654 orinas en nuestro hospital procedentes de pacientes con sospecha de ITU. Las muestras fueron procesadas por citometría de flujo y sembradas según criterios establecidos. Pasadas 48 h, se evaluó el crecimiento. Ante la sospecha de infección por Aerococcus spp/A. schaalii, se realizó un test de identificación con Vitek2® hasta 2014 y con MALDI-TOF desde 2015. Resultados: Durante el periodo de estudio se registraron 35 aislamientos de Aerococcus spp/A. schaalii correspondientes a 34 pacientes. Seis aislados se identificaron por Vitek2® y 29 por MALDI-TOF. De los 34 pacientes, 33 tenían como mínimo un factor de riesgo (>65 años, inmunosupresión o cáncer, anormalidades del tracto urinario, ITU recurrente, diabetes o cateterismo). Conclusiones: Desde la implementación del MALDI-TOF en el laboratorio, el aislamiento de Aerococcus spp/A. schaalii ha aumentado 5 veces. El perfil más afectado es el de un individuo de edad avanzada con ITU recurrentes y cáncer. Keywords: Urinary tract infection, Aerococcus spp, Actinotignum schaalii, MALDI-TOF, Palabras clave: Infección del tracto urinario, Aerococcus spp, Actinotignum schaalii, MALDI-TO

Reliable resolution of ambiguous hepatitis C virus genotype 1 results with the Abbott HCV Genotype Plus RUO assay

Accurate subtyping of hepatitis C virus genotype 1 (HCV-1) remains clinically and epidemiologically relevant. The Abbott HCV Genotype Plus RUO (GT Plus) assay, targeting the core region, was evaluated as a reflex test to resolve ambiguous HCV-1 results in a challenging sample collection. 198 HCV-1 specimens were analysed with GT Plus (38 specimens with and 160 without subtype assigned by the Abbott RealTime Genotype II (GT II) assay targeting the 5'NC and NS5B regions). Sanger sequencing of the core and/or NS5B regions were performed in 127 specimens without subtype assignment by GT II, with "not detected" results by GT Plus, or with mixed genotypes/subtypes. The remaining GT Plus results were compared to LiPA 2.0 (n = 45) or just to GT II results if concordant (n = 26). GT Plus successfully assigned the subtype in 142/160 (88.8%) samples. "Not detected" results indicated other HCV-1 subtypes/genotypes or mismatches in the core region in subtype 1b. The subtyping concordance between GT Plus and either sequencing or LiPA was 98.6% (140/142). Therefore, combined use of GT II and GT Plus assays represents a reliable and simple approach which considerably reduced the number of ambiguous HCV-1 results and enabled a successful subtyping of 98.9% of all HCV-1 samples