A combined approach of MALDI-TOF mass spectrometry and multivariate analysis as a potential tool for the detection of SARS-CoV-2 virus in nasopharyngeal swabs

Coronavirus disease 2019, known as COVID-19, is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The early, sensitive and specific detection of SARS-CoV-2 virus is widely recognized as the critical point in responding to the ongoing outbreak. Currently, the diagnosis is based on molecular real time RT-PCR techniques, although their implementation is being threatened due to the extraordinary demand for supplies worldwide. That is why the development of alternative and / or complementary tests becomes so relevant. Here, we exploit the potential of mass spectrometry technology combined with machine learning algorithms, for the detection of COVID-19 positive and negative protein profiles directly from nasopharyngeal swabs samples. According to the preliminary results obtained, accuracy =67.66 %, sensitivity =61.76 %, specificity =71.72 %, and although these parameters still need to be improved to be used as a screening technique, mass spectrometry- based methods coupled with multivariate analysis showed that it is an interesting tool that deserves to be explored as a complementary diagnostic approach due to the low cost and fast performance. However, further steps, such as the analysis of a large number of samples, should be taken in consideration to determine the applicability of the method developed.Fil: Rocca, María Florencia. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud "Dr. C. G. Malbrán"; Argentina. Universidad Nacional de Santiago del Estero. Facultad de Humanidades Ciencias Sociales y de la Salud. Instituto de Estudios e Investigaciones en Enfermería; Argentina. Red Nacional de Espectrometría de Masas Aplicada a la Microbiología Clínica; ArgentinaFil: Zintgraff, Jonathan Cristian. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud "Dr. C. G. Malbrán"; Argentina. Universidad Nacional de Santiago del Estero. Facultad de Humanidades Ciencias Sociales y de la Salud. Instituto de Estudios e Investigaciones en Enfermería; Argentina. Red Nacional de Espectrometría de Masas Aplicada a la Microbiología Clínica; ArgentinaFil: Dattero, María Elena. Universidad Nacional de Santiago del Estero. Facultad de Humanidades Ciencias Sociales y de la Salud. Instituto de Estudios e Investigaciones en Enfermería; Argentina. Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán". Instituto Nacional de Medicina Tropical; ArgentinaFil: Santos, Leonardo Silva. Universidad de Talca; ChileFil: Ledesma, Martin Manuel. Red Nacional de Espectrometría de Masas Aplicada A la Microbiología Clínica (renaem Argentina); Argentina. Universidad de Buenos Aires. Facultad de Medicina. Hospital de Clínicas General San Martín; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Vay, Carlos Alberto. Red Nacional de Espectrometría de Masas Aplicada a la Microbiología Clínica; Argentina. Universidad de Buenos Aires. Facultad de Medicina. Hospital de Clínicas General San Martín; ArgentinaFil: Prieto, Mónica Raquel. Red Nacional de Espectrometría de Masas Aplicada a la Microbiología Clínica; Argentina. Universidad de Buenos Aires; ArgentinaFil: Benedetti, Estefanía. Universidad Nacional de Santiago del Estero. Facultad de Humanidades Ciencias Sociales y de la Salud. Instituto de Estudios e Investigaciones en Enfermería; Argentina. Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán". Instituto Nacional de Medicina Tropical; ArgentinaFil: Avaro, Martín. Universidad Nacional de Santiago del Estero. Facultad de Humanidades Ciencias Sociales y de la Salud. Instituto de Estudios e Investigaciones en Enfermería; Argentina. Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán". Instituto Nacional de Medicina Tropical; ArgentinaFil: Russo, Mara Laura. Universidad Nacional de Santiago del Estero. Facultad de Humanidades Ciencias Sociales y de la Salud. Instituto de Estudios e Investigaciones en Enfermería; Argentina. Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán". Instituto Nacional de Medicina Tropical; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Nachtigall, Fabiane Manke. Universidad Autónoma de Chile; ChileFil: Baumeister, Elsa. Universidad Nacional de Santiago del Estero. Facultad de Humanidades Ciencias Sociales y de la Salud. Instituto de Estudios e Investigaciones en Enfermería; Argentina. Administración Nacional de Laboratorios e Institutos de Salud "Dr. Carlos G. Malbrán". Instituto Nacional de Medicina Tropical; Argentin

Prevalence of Pertussis Antibodies in Maternal Blood, Cord Serum, and Infants From Mothers With and Those Without Tdap Booster Vaccination During Pregnancy in Argentina

Fil: Fallo, Aurelia A. Department of Pediatric Infectious Diseases, School of Medicine, Hospital de Niños "Ricardo Gutiérrez," University of Buenos Aires; Argentina.Fil: Neyro, Silvina E. Department of Pediatric Infectious Diseases, School of Medicine, Hospital de Niños "Ricardo Gutiérrez," University of Buenos Aires; Argentina.Fil: Manonelles, Gabriela V. Department of Pediatric Infectious Diseases, School of Medicine, Hospital de Niños "Ricardo Gutiérrez," University of Buenos Aires; Argentina.Fil: Lara, Claudia. Administración Nacional de Laboratorios e Institutos de Salud “Dr. Carlos G. Malbrán” (ANLIS); Argentina.Fil: Hozbor, Daniela. Laboratorio VacSal, Instituto de Biotecnología y Biología Molecular (IBBM), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CCT-CONICET; Argentina.Fil: Zintgraff, Jonathan. Administración Nacional de Laboratorios e Institutos de Salud “Dr. Carlos G. Malbrán” (ANLIS); Argentina.Fil: Mazzeo, Silvina. Departments of Obstetrics and Gynecology, Hospital D. F. Santojanni, Buenos Aires; Argentina.Fil: Davison, Héctor E. Departments of Obstetrics and Gynecology, Hospital D. F. Santojanni, Buenos Aires; Argentina.Fil: González, Susana. Pediatrics, Hospital D. F. Santojanni, Buenos Aires; Argentina.Fil: Zapulla, Estella. Pediatrics, Hospital D. F. Santojanni, Buenos Aires; ArgentinaFil: Canle, Oscar. Blood Center, Hospital de Niños "Ricardo Gutiérrez," Buenos Aires; ArgentinaFil: Huespe, Miguel. Departments of Obstetrics and Gynecology, Hospital D. F. Santojanni, Buenos Aires; Argentina.Fil: Galas, Marcelo. Administración Nacional de Laboratorios e Institutos de Salud “Dr. Carlos G. Malbrán” (ANLIS); Argentina.Fil: López, Eduardo L. Department of Pediatric Infectious Diseases, School of Medicine, Hospital de Niños "Ricardo Gutiérrez," University of Buenos Aires; Argentina.Morbidity and mortality rates for pertussis in infants are high because disease often occurs before the onset of routine immunization or in those who do not complete a primary immunization series. Pertussis immunization is recommended during pregnancy to achieve antibody levels sufficient to protect young infants. To our knowledge, no previous reports of maternal pertussis immunization results in Latin America exist in the literature

The classical Bordetella species and MALDI-TOF technology: a brief experience

Fil: Zintgraff, Jonathan. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas. Departamento de Bacteriología. Servicio de Bacteriología Clínica; Argentina.Fil: Irazu, Lucía. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas. Departamento de Bacteriología. Servicio de Bacteriología Clínica; Argentina.Fil: Lara, Claudia. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas. Departamento de Bacteriología. Servicio de Bacteriología Clínica; Argentina.Fil: Rodriguez, Marcelo. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas. Departamento de Bacteriología. Servicio de Bacteriología Clínica; Argentina.Fil: Santos, Mauricio. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas. Departamento de Bacteriología. Servicio de Bacteriología Clínica; Argentina.The aim of this work was to evaluate and optimize the identification of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica (usually known as the classical Bordetella species) using Bruker Biotyper matrix-assisted laser desorption ionization/time-of-flight mass spectrometry (MALDI-TOF MS)

Utility of platforms Viteks MS and Microflex LT for the identification of complex clinical isolates that require molecular methods for their taxonomic classification

Fil: Rocca, María Florencia. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas. Departamento de Bacteriología. Servicio de Bacteriología Especial; Argentina.Fil: Barrios, Rubén. Laboratorio de Bacteriología, Hospital Italiano de Buenos Aires, Ciudad Autónoma de Buenos Aires; Argentina.Fil: Zintgraff, Jonathan. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas. Departamento de Bacteriología. Servicio de Bacteriología Clínica; Argentina.Fil: Martínez, Claudia. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas. Departamento de Bacteriología. Servicio de Bacteriología Especial; Argentina.Fil: Irazu, Lucía. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas; Argentina.Fil: Vay, Carlos. Instituto de Fisiopatología y Bioquímica Clínica, Hospital de Clínicas José de San Martín, Facultad de Farmacia y Bioquímica, Ciudad Autónoma de Buenos Aires; Argentina.Fil: Prieto, Mónica A. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas. Departamento de Bacteriología. Servicio de Bacteriología Especial; Argentina.Mass spectrometry has revolutionized the clinical microbiology field in America's and Europe's industrialized countries, for being a fast, reliable and inexpensive technique. Our study is based on the comparison of the performance of two commercial platforms, Microflex LT (Bruker Daltonics, Bremen, Germany) and Vitek MS (bioMérieux, Marcy l´Etoile, France) for the identification of unusual and hard-to-diagnose microorganisms in a Reference Laboratory in Argentina. During a four-month period (February-May 2018) the diagnostic efficiency and the concordance between both systems were assessed, and the results were compared with the polyphasic taxonomic identification of all isolates. The study included 265 isolates: 77 Gram-Negative Bacilli, 33 Gram-Positive Cocci, 40 Anaerobes, 35 Actinomycetales, 19 Fastidious Microorganisms and 61 Gram-Positive Bacilli. All procedures were practiced according to the manufacturer's recommendations in each case by duplicate, and strictly in parallel. Other relevant factors, such as the utility of the recommended extraction protocols, reagent stability and connectivity were also evaluated. Both systems correctly identified the majority of the isolates to species and complex level (82%, 217/265). Vitex MS achieved a higher number of correct species-level identifications between the gram-positive microorganisms; however, it presented greater difficulty in the identification of non-fermenting bacilli and a higher number of incorrect identifications when the profile of the microorganism was not represented in the commercial database. Both platforms showed an excellent performance on the identification of anaerobic bacteria and fastidious species. Both systems enabled the fast and reliable identification of most of the tested isolates and were shown to be very practical for the user

Utility of platforms Viteks MS and Microflex LT for the identification of complex clinical isolates that require molecular methods for their taxonomic classification

Fil: Rocca, María Florencia. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas. Departamento de Bacteriología. Servicio de Bacteriología Especial; Argentina.Fil: Barrios, Rubén. Laboratorio de Bacteriología, Hospital Italiano de Buenos Aires, Ciudad Autónoma de Buenos Aires; Argentina.Fil: Zintgraff, Jonathan. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas. Departamento de Bacteriología. Servicio de Bacteriología Clínica; Argentina.Fil: Martínez, Claudia. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas. Departamento de Bacteriología. Servicio de Bacteriología Especial; Argentina.Fil: Irazu, Lucía. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas; Argentina.Fil: Vay, Carlos. Instituto de Fisiopatología y Bioquímica Clínica, Hospital de Clínicas José de San Martín, Facultad de Farmacia y Bioquímica, Ciudad Autónoma de Buenos Aires; Argentina.Fil: Prieto, Mónica A. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas. Departamento de Bacteriología. Servicio de Bacteriología Especial; Argentina.Mass spectrometry has revolutionized the clinical microbiology field in America's and Europe's industrialized countries, for being a fast, reliable and inexpensive technique. Our study is based on the comparison of the performance of two commercial platforms, Microflex LT (Bruker Daltonics, Bremen, Germany) and Vitek MS (bioMérieux, Marcy l´Etoile, France) for the identification of unusual and hard-to-diagnose microorganisms in a Reference Laboratory in Argentina. During a four-month period (February-May 2018) the diagnostic efficiency and the concordance between both systems were assessed, and the results were compared with the polyphasic taxonomic identification of all isolates. The study included 265 isolates: 77 Gram-Negative Bacilli, 33 Gram-Positive Cocci, 40 Anaerobes, 35 Actinomycetales, 19 Fastidious Microorganisms and 61 Gram-Positive Bacilli. All procedures were practiced according to the manufacturer's recommendations in each case by duplicate, and strictly in parallel. Other relevant factors, such as the utility of the recommended extraction protocols, reagent stability and connectivity were also evaluated. Both systems correctly identified the majority of the isolates to species and complex level (82%, 217/265). Vitex MS achieved a higher number of correct species-level identifications between the gram-positive microorganisms; however, it presented greater difficulty in the identification of non-fermenting bacilli and a higher number of incorrect identifications when the profile of the microorganism was not represented in the commercial database. Both platforms showed an excellent performance on the identification of anaerobic bacteria and fastidious species. Both systems enabled the fast and reliable identification of most of the tested isolates and were shown to be very practical for the user

Distribution of PCV13 and PPSV23 Streptococcus pneumoniae serotypes in Argentinean adults with invasive disease, 2013-2017

Fil: Zintgraff, Jonathan. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas. Departamento de Bacteriología. Servicio de Bacteriología Clínica; Argentina.Fil: Fossati, M. S. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas. Departamento de Bacteriología. Servicio de Bacteriología Clínica; Argentina.Fil: Sorhouet Pereira, Cecilia. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas. Departamento de Bacteriología. Servicio de Bacteriología Clínica; Argentina.Fil: Veliz, Omar. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas. Departamento de Bacteriología. Servicio de Bacteriología Clínica; Argentina.Fil: Regueira, Mabel. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas. Departamento de Bacteriología. Servicio de Bacteriología Clínica; Argentina.Fil: Moscoloni, Maria Alicia. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas. Departamento de Bacteriología. Servicio de Bacteriología Clínica; Argentina.Fil: Irazu, Lucía. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas. Departamento de Bacteriología. Servicio de Bacteriología Clínica; Argentina.Fil: Lara, Claudia. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas. Departamento de Bacteriología. Servicio de Bacteriología Clínica; Argentina.Fil: Napoli, Daniela. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas. Departamento de Bacteriología. Servicio de Bacteriología Clínica; Argentina.Streptococcus pneumoniae is a major cause of severe invasive disease associated with high mortality and morbidity worldwide. To identify the serotypes most commonly associated with infection in adults in Argentina, 791 pneumococcal isolates from 56 hospitals belonging to 16 provinces and Buenos Aires city were serotyped. The isolates were submitted as part of a National Surveillance Program for invasive pneumococcal disease in adults, which started in 2013. Serotypes 3, 8, 12F, 7F and 1 were the most prevalent among adult patients. During the study period there was no significant difference in serotype distribution between the age groups studied (18-64 and ≥65 years old), except for serotype 1, 3 and 23A. Most prevalent serotypes in pneumonia were serotype 7F, 1, 12F, 8, and 3. When the clinical diagnosis was meningitis, serotype 3 and 12F were the most prevalent, whereas when the diagnosis was sepsis/bacteremia the most prevalent was serotype 8. In this work, for the 18-64-year-old group, PPSV23 and PCV13 serotypes accounted for 74.56% and 44.54% respectively of the cases in the studied period. On the other hand, for the ≥65-year-old group, these serotypes represented 72.30% and 41.42% respectively. The aim of this work was to establish the knowledge bases of the serotypes that cause invasive pneumococcal diseases in the adult population in Argentina and to be able to detect changes in their distribution over time in order to explore the potential serotype coverage of the vaccines in current use

Prevalence of Pertussis Antibodies in Maternal Blood, Cord Serum, and Infants From Mothers With and Those Without Tdap Booster Vaccination During Pregnancy in Argentina

Background Morbidity and mortality rates for pertussis in infants are high because disease often occurs before the onset of routine immunization or in those who do not complete a primary immunization series. Pertussis immunization is recommended during pregnancy to achieve antibody levels sufficient to protect young infants. To our knowledge, no previous reports of maternal pertussis immunization results in Latin America exist in the literature. Methods This study compared pertussis antibody levels in newborns from mothers who received or did not receive a tetanus-diphtheria-acellular pertussis vaccination (TdapV) during pregnancy. Each mother's level of immunoglobulin G antibodies against pertussis toxin (IgG-PT) was measured with a validated, specific enzyme-linked immunosorbent assay (ELISA). Results Paired mother and cord serum samples were compared in 105 mothers with and 99 mothers without a TdapV. At birth, the mothers with and those without a TdapV had serum IgG-PT geometric mean concentrations (GMCs) of 35.1 and 9.8 ELISA units (EU)/mL, respectively (P < .0001); cord blood GMCs were 51.3 and 11.6 EU/mL, respectively (P < .0003); and cord blood IgG-PT levels were <5 EU/mL in 2.9% and 16.1% of the cord blood samples, respectively (P < .001). The mothers received their TdapV at a mean (± standard deviation [SD]) of 24.7 ± 4.8 weeks' gestation. Vaccination timing did not affect the IgG-PT GMC at birth. Placental antibody transference efficiencies (measured as the ratio of the cord blood GMC to the maternal GMC) were 1.46 and 1.18 for mothers with and those without a TdapV, respectively. The IgG-PT GMCs were 17.7 EU/mL in 36 infants in their first month of life and 11.6 EU/mL in 32 infants in their second month of life. Conclusions Women who received a TdapV during pregnancy had significantly a higher serum/cord IgG-PT concentration at birth than mothers who did not receive a TdapV. Timing of the immunization was not correlated with antibody concentrations. Infants born to immunized mothers had significantly higher antibody levels during their first 2 months of life.Instituto de Biotecnología y Biología MolecularConsejo Nacional de Investigaciones Científicas y Técnica

Serotype Distribution of Remaining Pneumococcal Meningitis in the Mature PCV10/13 Period: Findings from the PSERENADE Project

Pneumococcal conjugate vaccine (PCV) introduction has reduced pneumococcal meningitis incidence. The Pneumococcal Serotype Replacement and Distribution Estimation (PSERENADE) project described the serotype distribution of remaining pneumococcal meningitis in countries using PCV10/13 for least 5-7 years with primary series uptake above 70%. The distribution was estimated using a multinomial Dirichlet regression model, stratified by PCV product and age. In PCV10-using sites (N = 8; cases = 1141), PCV10 types caused 5% of cases <5 years of age and 15% among ≥5 years; the top serotypes were 19A, 6C, and 3, together causing 42% of cases <5 years and 37% ≥5 years. In PCV13-using sites (N = 32; cases = 4503), PCV13 types caused 14% in <5 and 26% in ≥5 years; 4% and 13%, respectively, were serotype 3. Among the top serotypes are five (15BC, 8, 12F, 10A, and 22F) included in higher-valency PCVs under evaluation. Other top serotypes (24F, 23B, and 23A) are not in any known investigational product. In countries with mature vaccination programs, the proportion of pneumococcal meningitis caused by vaccine-in-use serotypes is lower (≤26% across all ages) than pre-PCV (≥70% in children). Higher-valency PCVs under evaluation target over half of remaining pneumococcal meningitis cases, but questions remain regarding generalizability to the African meningitis belt where additional data are needed