Beneath the surface: a case report on nonencapsulated Streptococcus pneumoniae-associated invasive disease in an immunocompromised patient.

Background: Streptococcus pneumoniae, a prominent human pathogen linked to various systemic diseases, includes non-typeable pneumococci marked by the absence of a detectable capsule. However, the majority of invasive infections are attributed to encapsulated strains. This case report details the first documented instance of invasive disease caused by non-typeable S. pneumoniae in Argentina since 2017. Case Presentation: A 19-year-old woman presented with haemorrhagic injuries attributed to chronic oral mucosa irritation. Subsequent hospitalization revealed bone marrow aplasia, leading to antibiotic, antifungal, antiviral, and immunosuppressive treatments, culminating in her discharge. Two weeks later, she was readmitted with sepsis related to a respiratory focus, exhibiting a negative COVID-PCR test. After ten days, ICU admission revealed additional infections: positive COVID-PCR test, fungal sinusitis, and S. pneumoniae bacteremia. Targeted treatments led to improvement, and the patient was subsequently discharged. S pneumoniae characterization: Verification of the capsule's absence utilized traditional methods such as the Quellung reaction, transmission electron microscopy, molecular assays, and Whole Genome Sequencing (WGS). The isolate, identified as ST18335, displayed genetic features and antibiotic resistance patterns, concordant between WGS and the agar dilution method. It demonstrated non-susceptibility to penicillin and cefotaxime, based on meningitis breakpoints, as well as meropenem and cotrimoxazole. Conclusion: This case underscores the clinical significance of non-typeable S. pneumoniae, emphasizing the necessity for a comprehensive approach to identification and characterization. The findings contribute to ongoing discussions regarding the challenges posed by non-typeable strains in vaccine development, understanding clinical impacts, and addressing antibiotic resistance. As the pneumococcal epidemiological landscape evolves, this case serves as a valuable addition to the evolving knowledge surrounding non-typeable S. pneumoniae, highlighting the continued need for surveillance and research in infectious diseases.

Exploring Streptococcus pneumoniae capsular typing through MALDI-TOF mass spectrometry and machine-learning algorithms in Argentina: Identifying prevalent NON PCV13 serotypes alongside PCV13 serotypes.

Introduction: Laboratory surveillance of Streptococcus pneumoniae serotypes plays a crucial role in effectively implementing vaccines to prevent invasive pneumococcal diseases. The conventional method of serotyping, known as the Quellung reaction, is both time-consuming and expensive. However, the emergence of MALDI-TOF MS technology has revolutionized microbiology laboratories by enabling rapid and cost-effective serotyping based on protein profiles. Objectives: In this study, we aimed to investigate the viability of utilizing MALDI-TOF MS technology as an adjunctive and screening method for capsular typing of Streptococcus pneumoniae. Our approach involved developing classification models based on MALDI-TOF MS to discern between Streptococcus pneumoniae strains originating from PCV13 (13-valent pneumococcal conjugate vaccine) and NON PCV13 isolates. Methods: Firstly, we established a comprehensive spectral database comprising isolates of serotypes present in the PCV13 vaccine, along with the top 10 most prevalent NON PCV13 serotypes based on local epidemiological data. This database served as a foundation for developing unsupervised models utilizing MALDI-TOF MS spectra, which enabled us to identify inherent patterns and relationships within the data. Our analysis involved a dataset comprising 215 new isolates collected from nationwide surveillance in Argentina. Our approach involved developing classification models based on MALDI-TOF MS to discern between Streptococcus pneumoniae strains originating from PCV13 (13-valent pneumococcal conjugate vaccine) and NON PCV13 isolates. Results: Although our findings revealed suboptimal performance in serotype classification, they provide valuable insights into the potential of machine learning algorithms in this context. The sensitivity of the models ranged from 0.41 to 0.46, indicating their ability to detect certain serotypes. The observed specificity consistently remained at 0.60, suggesting a moderate level of accuracy in identifying non-vaccine serotypes. These results highlight the need for further refinement and optimization of the algorithms to enhance their discriminative power and predictive accuracy in serotype identification.By addressing the limitations identified in this study, such as exploring alternative feature selection techniques or optimizing algorithm parameters, we can unlock the full potential of machine learning in robust and reliable serotype classification of S. pneumoniae. Our work not only provides a comprehensive evaluation of multiple machine learning models but also emphasizes the importance of considering their strengths and limitations. Conclusion: Overall, our study contributes to the growing body of research on utilizing MALDI-TOF MS and machine learning algorithms for serotype identification purposes.

Rapid and accurate detection of Shiga toxin-producing Escherichia coli (STEC) serotype O157 : H7 by mass spectrometry directly from the isolate, using 10 potential biomarker peaks and machine learning predictive models.

Introduction. The different pathotypes of Escherichia coli can produce a large number of human diseases. Surveillance is complex since their differentiation is not easy. In particular, the detection of Shiga toxin-producing Escherichia coli (STEC) serotype O157 : H7 consists of stool culture of a diarrhoeal sample on enriched and/or selective media and identification of presumptive colonies and confirmation, which require a certain level of training and are time-consuming and expensive.Hypothesis. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a quick and easy way to obtain the protein spectrum of a microorganism, identify the genus and species, and detect potential biomarker peaks of certain characteristics.Aim. To verify the usefulness of MALDI-TOF MS to rapidly identify and differentiate STEC O157 : H7 from other E. coli pathotypes.Methodology. The direct method was employed, and the information obtained using Microflex LT platform-based analysis from 60 clinical isolates (training set) was used to detect differences between the peptide fingerprints of STEC O157 : H7 and other E. coli strains. The protein profiles detected laid the foundations for the development and evaluation of machine learning predictive models in this study.Results. The detection of potential biomarkers in combination with machine learning predictive models in a new set of 142 samples, called 'test set', achieved 99.3 % (141/142) correct classification, allowing us to distinguish between the isolates of STEC O157 : H7 and the other E. coli group. Great similarity was also observed with respect to this last group and the Shigella species when applying the potential biomarkers algorithm, allowing differentiation from STEC O157 : H7Conclusion. Given that STEC O157 : H7 is the main causal agent of haemolytic uremic syndrome, and based on the performance values obtained in the present study (sensitivity=98.5 % and specificity=100.0 %), the implementation of this technique provides a proof of principle for MALDI-TOF MS and machine learning to identify biomarkers to rapidly screen or confirm STEC O157 : H7 versus other diarrhoeagenic E. coli in the future.

Invasive Streptococcus pneumoniae isolates from pediatric population in Argentina for the period 2006-2019. Temporal progression of serotypes distribution and antibiotic resistance.

Streptococcus pneumoniae is a major cause of severe invasive disease associated with high mortality and morbidity worldwide. A total of 2908 pneumococcal isolates were analyzed between 2006 and 2019. Gold standard pneumococcal serotyping (the Neufeld-Quellung reaction) was performed to identify the serotypes associated with infection in children < 5 years in Argentina and agar dilution method was carried out to determine their profiles to 14 antimicrobial agents. In 2012, the 13-valent pneumococcal conjugate vaccine (PCV13) was included in the National Immunization Program. In this work we have analyzed the local epidemiology of invasive pneumococcal diseases before and after the introduction of this vaccine in order to understand the epidemiological relevance and impact of PCV13. During the periods compared in the present study there was a significant increase in the proportion of non-PCV13 serotypes, serogroup 24 (246.7%) and 12F (85.7%), and a significant decrease in PCV13 serotypes, including serotypes 14 (91.2%), 5 (95.6%) and 1 (84.6%) among others. Another observation was that serotypes 3 (7.4%) and 19A (4.9%) still remain among the most frequent serotypes despite being part of the PCV13 formulation. Regarding antimicrobial resistance, in the present study we observed an increase in erythromycin resistance during the period of study mainly associated to serotype 14 in the pre-PCV13 period and to serogroup 24 in the post-PCV13 period, which also was the major NVT serotype associated with antimicrobial resistance and MDR. Serotypes 14, 24A/B/F and 19A were in the first three places among isolates resistant to all the antibiotics tested. Our data highlight the importance of continuous surveillance to assess the impact of pneumococcal vaccines and the use of antibiotics in the dynamic of pneumococcal serotypes.

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.

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.

Distribution of PCV13 and PPSV23 Streptococcus pneumoniae serotypes in Argentinean adults with invasive disease, 2013-2017 / Distribución de los serotipos PCV13 y PPSV23 de Streptococcus pneumoniae en adultos argentinos con enfermedad invasiva, 2013-2017

Abstract 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 sep-sis/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.

Resumen Streptococcus pneumoniae es una causa importante de enfermedad invasiva grave asociada con una alta mortalidad y morbilidad en todo el mundo. Para identificar los serotipos principales asociados con la infección en adultos en Argentina, 791 aislamientos de neumococo de 56 hospitales pertenecientes a 16 provincias y la ciudad de Buenos Aires fueron serotipificados. Los aislamientos fueron remitidos como parte del Programa Nacional de Vigilancia para la enfermedad neumocócica invasiva en adultos, que comenzó en 2013. Los serotipos 3, 8, 12F, 7F y 1 fueron los más prevalentes. Durante el período de estudio no hubo diferencias significativas en la distribución de serotipos entre los dos grupos de adultos estudiados (18-64 y >65 años), excepto para los serotipos 1, 3 y 23A. Los serotipos más prevalentes en casos de neumonía fueron 7F, 1, 12F, 8 y 3. Cuando el diagnóstico clínico fue meningitis, los serotipos 3 y 12F fueron los más prevalentes. Y el serotipo 8 fue el más prevalente en la sepsis/bacteriemia. En el grupo de 18-64 años, los serotipos PPSV23 y PCV13 representaron, respectivamente, el 74,56 y el 44,54% de los casos de enfermedad invasiva en el período estudiado. En el grupo de >65 años, estos serotipos representaron el 72,30 y 41,42%, respectivamente. Es importante conocer los serotipos causantes de infecciones neumocócicas invasivas en la población adulta en Argentina y detectar eventuales cambios en su distribución a lo largo del tiempo, para explorar la potencial cobertura de las vacunas utilizadas.

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

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.

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

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.

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

PURPOSE: 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). METHODOLOGY: A set of 106 previously characterized clinical isolates was used. The results were interpreted according to the manufacturer's recommendations and, in addition, a new score value cutoff was used for species identification. Further, the 10 % rule (previously adopted by other authors) and the new 5 % breaking point (proposed in this work) were evaluated in order to optimize identification rates.Results/Key findings. Our results suggest that it is possible to distinguish different species of the classical Bordetella species by following a simple algorithm without additional testing being required. CONCLUSION: MALDI-TOF might be a reliable tool for the identification of this group of bacteria when a combination of cutoff scores is used. This procedure allows us to increase the identification rates for the classical Bordetella species significantly; however, more studies will be required to determine the applicability of the method to other difficult-to-distinguish organisms.

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.

Activity of the colistin-rifampicin combination against colistin-resistant, carbapenemase-producing Gram-negative bacteria.

Colistin (COL) is one of the few antimicrobials that retain activity against carbapenemase-producing Gram-negative bacteria (GNB). However, the emergence of COL resistance has renewed the use of combination therapy. The aim of this study was to determine the activity of COL plus rifampicin (RIF) against clinical isolates of COL-resistant, carbapenemase-producing GNB. We employed 36 COL-resistant carbapenemase-producing isolates (27 Klebsiella pneumoniae, 5 Serratia marcescens, and 4 Acinetobacter baumannii) belonging to 36 patients. E-test/agar dilution of all strains was performed with E-test strips of COL placed on agar plates with and without RIF. In 11 patients, the synergy was confirmed by time-kill studies. Synergy was detected in 34 isolates, whereas indifference was detected in two S. marcescens. The E-test/agar dilution method showed comparable results to the time-kill studies. Seven patients infected with these isolates (two meningitis, four sepsis, and one urinary tract infection) were treated with the combination successfully.