[Molecular characterization of Listeria monocytogenes isolates from human and food sources in Argentina, 2018-2023]. / Caracterización molecular de aislamientos de Listeria monocytogenes de origen humano y alimentario en Argentina, 2018-2023.

Human listeriosis is an infectious disease caused by Listeria monocytogenes. The invasive form of this disease leads to a high rate of hospitalizations and fatality. The main mode of transmission is through contaminated ready-to-eat foods such as dairy, vegetables and meat products. The knowledge of the diversity and population dynamics of isolates collected from human and food sources is essential for the detection of clusters and the identification of common sites of infection. The aim of this study was the molecular characterization of L. monocytogenes isolates in Argentina. We sequenced a total of 63 isolates, 35 from human and 28 from food sources, collected between 2018 and 2023. Our genomic study divided the isolates into two lineages, four serogroups, 17 sequence types and 15 clonal complexes (CCs). The hypervirulent clone CC1 (lineage I; serogroup IVb) predominated in human and food samples. The phylogenomic analysis showed a high and possible epidemiological relationship between isolates from human and/or food sources, suggesting the presence of transmission chains in our country. These findings highlight the need to strengthen genomic surveillance of L. monocytogenes in Argentina. The identification of geographic distribution and characteristics of predominant and emerging clones from human and food sources might help to focus action plans and public health policies better directed at the control and prevention of listeriosis.

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.

Enfermedad del legionario en Argentina: evolución de la estrategia diagnóstica en el laboratorio / Legionnaires' disease in Argentina: Evolution of the laboratory diagnostic strategy

Resumen La enfermedad del legionario (EL) es una neumonía aguda grave, que ocurre espo-rádicamente o como epidemias, y que, generalmente, requiere hospitalización. El objetivo deeste trabajo fue describir la experiencia en el abordaje diagnóstico de laboratorio de la ELen Argentina durante el período 2016-2021. Se analizaron 168 especímenes clínicos correspondientes a 93 casos de neumonía con sospecha de EL. Las pruebas de laboratorio incluyeron ladeterminación del antígeno soluble de Legionella pneumophila serogrupo 1 en orina, la detec-ción de ADN de Legionella spp. en secreciones respiratorias bajas, por métodos moleculares convencionales y comerciales de tipo sindrómico, y el cultivo en medio selectivo. Se confirmó EL en 12 pacientes. El antígeno urinario confirmó el diagnóstico de 8 de ellos. Se recuperó L. pneumophila mediante el cultivo del material respiratorio de 6 pacientes que correspondieron a casos de neumonía asociada a cuidados de la salud y que fueron previamente diagnosticados por el método molecular comercial. La mitad de ellos no presentó antigenuria detectable. En un único paciente no hubo antigenuria detectable ni recuperación de Legionella en cultivo, y la confirmación de EL se basó en la detección de ADN de Legionella spp. por PCR en secreción respiratoria y el vínculo epidemiológico con otro caso de EL confirmado por cultivo. La detección del antígeno urinario es la prueba diagnóstica de primera línea. Sin embargo, la incorporación de métodos moleculares complementarios ha demostrado evitar falsos negativos y contribuir a un mejor conocimiento de la verdadera incidencia de la enfermedad.

Abstract Legionnaires' disease (LD) is severe acute pneumonia that occurs in sporadic or epidemic form, and generally requires hospitalizaron. The objective of this work was to describe the experience in the LD laboratory diagnostic approach in Argentina during the period 2016-2021. The laboratory analyzed 168 clinical specimens from 93 cases of suspected LD pneu-monia. Laboratory tests included the detection of the soluble antigen of Legionella pneumophila serogroup 1 in urine sample, detection of DNA of Legionella spp. in lower respiratory secre-tions by conventional and commercial molecular methods and isolation in selective medium. LD was confirmed in 12 patients. The urinary antigen allowed the diagnosis for 8 patients. L. pneumophila was isolated from the respiratory material of 6 patients suffering from health care-associated pneumonia, who had been previously diagnosed using the commercial molecular method. Fifty percent of these cases did not show detectable urinary antigen. A single patient did not shows neither detectable antigenuria nor isolation of Legionella from the respiratory sample and was diagnosed as a confirmed case of LD by the detection of DNA of Legionella spp. by PCR directly from the respiratory secretion and the epidemiological link with another case of confirmed LD by culture. Urinary antigen detection is the first-line diagnostic test. However, the incorporation of complementary molecular methods has proved to avoid false negatives and contributed to a better understanding of the true incidence of the disease.

[Legionnaires' disease in Argentina: Evolution of the laboratory diagnostic strategy]. / Enfermedad del legionario en Argentina: evolución de la estrategia diagnóstica en el laboratorio.

Legionnaires' disease (LD) is severe acute pneumonia that occurs in sporadic or epidemic form, and generally requires hospitalization. The objective of this work was to describe the experience in the LD laboratory diagnostic approach in Argentina during the period 2016-2021. The laboratory analyzed 168 clinical specimens from 93 cases of suspected LD pneumonia. Laboratory tests included the detection of the soluble antigen of Legionella pneumophila serogroup 1 in urine sample, detection of DNA of Legionella spp. in lower respiratory secretions by conventional and commercial molecular methods and isolation in selective medium. LD was confirmed in 12 patients. The urinary antigen allowed the diagnosis for 8 patients. L. pneumophila was isolated from the respiratory material of 6 patients suffering from health care-associated pneumonia, who had been previously diagnosed using the commercial molecular method. Fifty percent of these cases did not show detectable urinary antigen. A single patient did not shows neither detectable antigenuria nor isolation of Legionella from the respiratory sample and was diagnosed as a confirmed case of LD by the detection of DNA of Legionella spp. by PCR directly from the respiratory secretion and the epidemiological link with another case of confirmed LD by culture. Urinary antigen detection is the first-line diagnostic test. However, the incorporation of complementary molecular methods has proved to avoid false negatives and contributed to a better understanding of the true incidence of the disease.

Desarrollo y evaluación de una base de datos in house para la identificación rápida de Burkholderia contaminons por EM MALDI-TOF / Development and evaluation of an in-house database for quick identification of Burkholderia contaminans by MALDI-TOF MS

La espectrometría de masas (EM) (matrix assisted laser desorption ionization-time of flight) MALDI-TOF demostró ser una herramienta robusta para la identificación de numerosos grupos taxonómicos. No obstante, presenta limitaciones. Una ventaja clave de la técnica es la flexibilidad para la incorporación de espectros proteicos de microorganismos ausentes en la base de datos comercial. Dada la prevalencia de Burkholderia contaminans en los pacientes fibroquísticos en Argentina, y a que en ellos es crucial el diagnóstico microbiológico rápido y confiable, la EM MALDI-TOF surge como una herramienta estratégica. El objetivo del trabajo fue desarrollar una base de datos adicional con espectros peptídicos de aislamientos de referencia de B. contaminans. La misma demostró ser exitosa para la identificación del 97% de los aislamientos analizados. Por lo cual la EM MALDI-TOF con la base de datos extendida resultó ser una herramienta útil para la identificación y diferenciación de otras especies relacionadas a B. contaminans.

MALDI-TOF (matrix assisted laser desorption ionization-time of flight) mass spectrometry (MS) proved to be a robust tool for the identification of numerous taxonomic groups. However, it has limitations. A key advantage of this technique is the flexibility for the incorporation of protein profiles of microorganisms not included in the commercial database. Due to the prevalence of Burkholderia contaminans in fibrocystic patients in Argentina and the fact that rapid and reliable microbiological diagnosis is crucial in them, MALDI-TOF MS emerges as a strategic tool. The aim of this work was to develop an additional database with peptide spectra of reference isolates of B. contaminans. This database demonstrated to be successful for the identification of 97% of the isolates analyzed. Therefore, MALDI-TOF MS with the extended database was a useful tool for the identification and differentiation of other related species to B. contaminans.

[Development and evaluation of an in-house database for quick identification of Burkholderia contaminans by MALDI-TOF MS]. / Desarrollo y evaluación de una base de datos in house para la identificación rápida de Burkholderia contaminans por EM MALDI-TOF.

MALDI-TOF (matrix assisted laser desorption ionization-time of flight) mass spectrometry (MS) proved to be a robust tool for the identification of numerous taxonomic groups. However, it has limitations. A key advantage of this technique is the flexibility for the incorporation of protein profiles of microorganisms not included in the commercial database. Due to the prevalence of Burkholderia contaminans in fibrocystic patients in Argentina and the fact that rapid and reliable microbiological diagnosis is crucial in them, MALDI-TOF MS emerges as a strategic tool. The aim of this work was to develop an additional database with peptide spectra of reference isolates of B. contaminans. This database demonstrated to be successful for the identification of 97% of the isolates analyzed. Therefore, MALDI-TOF MS with the extended database was a useful tool for the identification and differentiation of other related species to B. contaminans.

Prevalencia de especies del complejo Burkholderia cepacia en pacientes con fibrosis quística en Argentina durante el período 2011-2015 / Prevalence of Burkholderia cepacia complex species in cystic fibrosis patients in Argentina during the period 2011-2015

Introducción: En la actualidad el complejo Burkholderia cepacia (B. cepacia) está compuesto por 20 especies filogenéticamente muy relacionadas. Algunas especies han emergido como patógenos oportunistas en pacientes inmunocomprometidos y son responsables de brotes intrahospitalarios. El complejo B. cepacia es un reconocido patógeno respiratorio en pacientes con fibrosis quística. B. cenocepacia y Burkholderia multivorans (B. multivorans) son las especies prevalentes en el mundo, según la literatura. Sin embargo, grupos de investigación en Argentina han descripto una epidemiología local particular, con prevalencia de la especie Burkholderia contaminans (B. contaminans). Métodos: Se estudiaron 68 aislamientos del complejo B. cepacia aislados de 46 pacientes con fibrosis quística de 14 hospitales distribuidos en 9 provincias del país. La identificación se llevó a cabo por métodos fenotípicos convencionales y fue confirmada por secuenciación parcial del gen recA. Los alineamientos de las secuencias se realizaron mediante el programa BLAST y fueron comparadas con las secuencias de las cepas tipo de cada una de las especies del complejo B. cepacia. Se determinó el perfil de sensibilidad a 4 agentes antimicrobianos para los aislamientos de las especies más prevalentes, según lo recomendado por la norma CLSI M45. Resultados: La especie prevalente resultó B. contaminans (49%, n = 33) seguida por B. cenocepacia (25%; n = 17). El resto de las especies identificadas fueron: Burkholderia seminalis (B. seminalis) (7%; n = 5), B. cepacia (7%; n = 5), B. multivorans (6%; n = 4), Burkholderia vietnamensis (5%, n = 3) y Burkholderia pyrrocinia (1%; n = 1). El 46% de los aislamientos de B. contaminans fueron resistentes a SXT y el 76% sensible a MIN, MEM y CAZ. Los aislamientos de B. cenocepacia fueron 100% resistentes a SXT y MIN, y el 47% a CAZ y MEM. En B. seminalis se observa un alto nivel de resistencia a TMS (80%), CAZ (60%) y MIN (60%), y un 60% de los aislamientos mostraron sensibilidad intermedia a MEM. Conclusión: Los únicos países que han documentado la prevalencia de B. contaminans en infecciones respiratorias de pacientes fibroquísticos por complejo B. cepacia son Argentina, España y Portugal, y recientemente se reportó un caso de 2 pacientes con fibrosis quística en Irlanda. Debido a la alta frecuencia con que B. contaminans es aislada en nuestro país, es necesario promover la investigación de las posibles fuentes de infección y comprender los factores y mecanismos implicados en la aparente mayor transmisibilidad de esta especie. Se observaron distintos patrones de sensibilidad entre las especies estudiadas

Introduction: Burkholderia cepacia (B. cepacia) complex is composed of 20 phylogenetically closely related bacterial species. Some species have emerged as opportunistic pathogens in immunocompromised patients and are responsible for nosocomial outbreaks. The B. cepacia complex is a recognized respiratory pathogen in patients with cystic fibrosis. Burkholderia cenocepacia and Burkholderia multivorans (B. multivorans) are the most prevalent species in the world, according to the literature. However, research groups in Argentina have described a particular local epidemiology, with prevalence of Burkholderia contaminans (B. contaminans). Methods: A total of 68 isolates of B. cepacia complex recovered of 46 cystic fibrosis patients attended at 14 hospitals distributed in 9 provinces of the country were studied. Identification was carried out by conventional phenotypic methods and was confirmed by recA gene sequencing. Sequences were analysed using the BLASTN program and comparing with B. cepacia complex type strains sequences deposited in GenBank. Antibiotic susceptibility tests were performed on isolates of the most prevalent species according to CLSI M45 guidelines. Results: The prevalent specie was B. contaminans (49%, n = 33) followed by B. cenocepacia (25%; n = 17). The remaining species were Burkholderia seminalis (B. seminalis) (7%, n = 5), B. cepacia (7%, n = 5), B. multivorans (6%, n = 4), Burkholderia vietnamensis (5%, n=3) and Burkholderia pyrrocinia (1%; n = 1). The 46% of B. contaminans isolates were resistant to SXT and 76% sensitive to MIN, MEM and CAZ. The isolates of B. cenocepacia were 100% resistant to SXT and MIN and 47% to CAZ and MEM. B. seminalis showed high levels of resistance to TMS (80%), CAZ (60%) and MIN (60%), and 60% of the isolates showed intermediate sensitivity to MEM. Conclusion: Previous reports have described the prevalence of B. contaminans isolation from cystic fibrosis patients in Argentina, Spain and Portugal, and a case of two patients with cystic fibrosis in Ireland has recently been reported. Due to the high frequency with which B. contaminans is isolated in our country, it is necessary to promote the investigation of possible sources of infection and to understand the factors and mechanisms involved in the apparent greater transmissibility of this species. Different antimicrobial resistance profiles were detected between the species

Prevalence of Burkholderia cepacia complex species in cystic fibrosis patients in Argentina during the period 2011-2015. / Prevalencia de especies del complejo Burkholderia cepacia en pacientes con fibrosis quística en Argentina durante el período 2011-2015.

INTRODUCTION: Burkholderia cepacia (B. cepacia) complex is composed of 20 phylogenetically closely related bacterial species. Some species have emerged as opportunistic pathogens in immunocompromised patients and are responsible for nosocomial outbreaks. The B. cepacia complex is a recognized respiratory pathogen in patients with cystic fibrosis. Burkholderia cenocepacia and Burkholderia multivorans (B. multivorans) are the most prevalent species in the world, according to the literature. However, research groups in Argentina have described a particular local epidemiology, with prevalence of Burkholderia contaminans (B. contaminans). METHODS: A total of 68 isolates of B. cepacia complex recovered of 46 cystic fibrosis patients attended at 14 hospitals distributed in 9 provinces of the country were studied. Identification was carried out by conventional phenotypic methods and was confirmed by recA gene sequencing. Sequences were analysed using the BLASTN program and comparing with B. cepacia complex type strains sequences deposited in GenBank. Antibiotic susceptibility tests were performed on isolates of the most prevalent species according to CLSI M45 guidelines. RESULTS: The prevalent specie was B. contaminans (49%, n = 33) followed by B. cenocepacia (25%; n = 17). The remaining species were Burkholderia seminalis (B. seminalis) (7%, n = 5), B. cepacia (7%, n = 5), B. multivorans (6%, n = 4), Burkholderia vietnamensis (5%, n=3) and Burkholderia pyrrocinia (1%; n = 1). The 46% of B. contaminans isolates were resistant to SXT and 76% sensitive to MIN, MEM and CAZ. The isolates of B. cenocepacia were 100% resistant to SXT and MIN and 47% to CAZ and MEM. B. seminalis showed high levels of resistance to TMS (80%), CAZ (60%) and MIN (60%), and 60% of the isolates showed intermediate sensitivity to MEM. CONCLUSION: Previous reports have described the prevalence of B. contaminans isolation from cystic fibrosis patients in Argentina, Spain and Portugal, and a case of two patients with cystic fibrosis in Ireland has recently been reported. Due to the high frequency with which B. contaminans is isolated in our country, it is necessary to promote the investigation of possible sources of infection and to understand the factors and mechanisms involved in the apparent greater transmissibility of this species. Different antimicrobial resistance profiles were detected between the species.