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1.
Infect Prev Pract ; 6(3): 100379, 2024 Sep.
Article in English | MEDLINE | ID: mdl-39006243

ABSTRACT

Members of the genus Phytobacter (order Enterobacterales) are isolated from the natural environment and clinical settings. Identification of Phytobacter strains based on biochemical characteristics is complicated due to taxonomic confusion, and they are often misidentified by automated identification systems in laboratories. In this study we describe the first three clinical cases associated with Phytobacter spp. reported in Argentina. We describe the identification, the molecular analysis using whole genome sequencing and the potential clinical relevance.

2.
Rev Argent Microbiol ; 56(3): 329-335, 2024.
Article in Spanish | MEDLINE | ID: mdl-38834434

ABSTRACT

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.


Subject(s)
Food Microbiology , Listeria monocytogenes , Listeriosis , Humans , Argentina/epidemiology , Listeria monocytogenes/genetics , Listeria monocytogenes/isolation & purification , Listeria monocytogenes/classification , Listeriosis/microbiology , Listeriosis/epidemiology , Phylogeny
3.
Pathogens ; 12(7)2023 Jul 21.
Article in English | MEDLINE | ID: mdl-37513808

ABSTRACT

OBJECTIVE: We aimed to describe a colistin (COL)-resistant (R) Chromobacterium violaceum (Cvi) isolate from a septic patient in Argentina expressing a previously unknown gene, blaCVI-1. METHODS: In 2019, a 12 year old child was injured with a thorn in a lagoon. The child was hospitalized due to sepsis and multiple abscesses. Cvi was isolated from skin and soft tissue and tracheal aspirate. The patient was successfully treated with imipenem (IMI) plus amikacin. Antimicrobial susceptibility was assessed by disk diffusion, broth microdilution, and the E-test. Carbapenemase activity was assayed by double-disk synergy and microbiological tests. Resistance, virulence, and additional gene searches were performed by in silico analysis of sequences obtained by whole-genome sequencing (WGS). A maximum likelihood phylogenetic tree was built with public Cvi genomes. RESULTS: R was seen for IMI and COL. Expression of a metallo-ß-lactamase was confirmed. Genome analysis revealed blaCVI-1, a subclass B2 metallo-ß-lactamase with 62.66% ID with CphA from A. hydrophila (WP081086394). R to COL could be attributed to the arnC and arnT genes. Virulence factors required for invasion and toxicity were also found. No plasmids were detected. The phylogeny tree showed two main clades with geographical distinction, and the isolate studied here stands alone in a branch closely related to two clinical isolates from the USA. CONCLUSIONS: This is the second report of infection by Cvi in Argentina. This pathogen carried a new gene, blaCVI-1, a metallo-ß-lactamase that can be detected by routine methods. Prompt suspicion of C. violaceum infection is crucial to treating this rare pathogen rapidly and properly.

4.
Acta bioquím. clín. latinoam ; Acta bioquím. clín. latinoam;57(2): 203-210, jun. 2023.
Article in Spanish | LILACS-Express | LILACS | ID: biblio-1519866

ABSTRACT

Resumen Haemophilus parainfluenzae forma parte de la microbiota normal de la cavidad oral y del tracto respiratorio superior. Es un reconocido agente causal de endocarditis y, con menor frecuencia, de enfermedades como neumonía, sepsis, osteomielitis, celulitis, meningitis y gastroenteritis aguda. Aquí se presenta un caso de orquiepididimitis en un joven adulto donde H. parainfluenzae, confirmado por espectrometría de masas (MALDI-TOF MS), fue el único patógeno detectado. Este caso contribuye a valorar el rol de H. parainfluenzae como patógeno humano, aislado a partir de sitios diferentes del torrente sanguíneo y las vías respiratorias.


Abstract Haemophilus parainfluenzae is part of the normal microbiota of the oral cavity and the upper respiratory tract. It is a recognised causal agent of endocarditis and, less frequently, of diseases such as pneumonia, sepsis, osteomyelitis, cellulitis, meningitis, and acute gastroenteritis. A case of orchiepididymitis in a young adult is reported, where H. parainfluenzae, confirmed by mass spectrometry (MALDI-TOF MS), was the only pathogen detected. This case contributes to assess the role of H. parainfluenzae as a human pathogen, isolated from sites other than the bloodstream and the respiratory tract.


Resumo Haemophilus parainfluenzae faz parte da microbiota normal da cavidade oral e do trato respiratório superior. É um reconhecido agente causal de endocardite e, menos frequentemente, de doenças como pneumonia, sepse, osteomielite, celulite, meningite e gastroenterite aguda. Aqui é relatado um caso de orquiepididimite em um adulto jovem onde H. parainfluenzae, confirmado por espectrometria de massa (MALDI-TOF MS), foi o único patógeno detectado. Este caso contribui para avaliar o papel do H. parainfluenzae como patógeno humano, isolado de outros locais que não sejam a corrente sanguínea e o trato respiratório.

5.
Rev. argent. microbiol ; Rev. argent. microbiol;55(2): 8-8, jun. 2023. graf
Article in Spanish | LILACS-Express | LILACS | ID: biblio-1449406

ABSTRACT

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.

6.
J Med Microbiol ; 72(5)2023 May.
Article in English | MEDLINE | ID: mdl-37130048

ABSTRACT

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.


Subject(s)
Escherichia coli Infections , Escherichia coli O157 , Shiga-Toxigenic Escherichia coli , Humans , Escherichia coli O157/metabolism , Serogroup , Escherichia coli Infections/diagnosis , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Biomarkers/metabolism
7.
Ciudad Autónoma de Buenos Aires; Ministerio de Salud de la Nación; 2023 Abril. 28 p.
Monography in Spanish | ARGMSAL, BINACIS | ID: biblio-1531716

ABSTRACT

La enfermedad de los legionarios es un importante problema de salud pública particularmente por su frecuente presentación en forma de brotes, tanto comunitarios como nosocomiales, y por su letalidad, especialmente en personas de edad avanzada o con otras enfermedades. La notificación oportuna de casos y/o brotes de enfermedad y la investigación epidemiológica permiten la identificación de la/s fuentes de exposición y la adopción de medidas de prevención y control adecuadas. Las infecciones por Legionella son más frecuentes entre adultos mayores de 50 años, hombres, fumadores y huéspedes inmunocomprometidos o con ciertas enfermedades crónicas subyacentes. La infección en niñas/os es rara, con ≤ 1% de los casos de neumonía causada por Legionella, y puede ser asintomática o leve y no detectada. La Legionella puede multiplicarse si el agua no es tratada de manera adecuada o si los sistemas de agua no son mantenidos adecuadamente.


Subject(s)
Legionellosis/prevention & control , Legionellosis/drug therapy , Disease Outbreaks , Epidemiological Monitoring
8.
Rev. argent. microbiol ; Rev. argent. microbiol;55(1): 51-60, mar. 2023.
Article in English | LILACS-Express | LILACS | ID: biblio-1441185

ABSTRACT

Abstract This is the first study of the genetic diversity of Moraxella spp. Isolates were detected in an Eye Hospital in the City of Buenos Aires. Due to the high frequency of Moraxella spp. observed in corneal abscesses, we decided to validate their identification at the species level, determine their drug susceptibility and perform molecular subtyping. Seventeen (17) isolates obtained from corneal abscesses were evaluated. The identification was carried out using a combination of biochemical tests and MALDI-TOF mass spectrometry. Of these isolates, 88.2% were identified as Moraxella lacunata, and 11.8% as Moraxella nonliquefaciens. Molecular subtyping was performed using the pulsed-field gel electrophoresis (PFGE) technique. All isolates were typable and thirteen digestion patterns were identified. Based on the obtained results, the PFGE technique using the SmaI enzyme can be used for epidemiological studies of strains of these species.


Resumen En este trabajo se presenta el primer estudio de diversidad genética de aislamientos de Moraxella spp. detectados en un hospital de oftalmología de la Ciudad Autónoma de Buenos Aires. Debido a la observación de una elevada frecuencia de Moraxella spp. en abscesos corneales, se decidió confirmar su identificación a nivel de especie, conocer su sensibilidad y realizar la subtipificación molecular. Se analizaron 17 aislamientos provenientes de abscesos corneales. La identificación se realizó mediante una combinación de pruebas bioquímicas y espectrometría de masas, MALDI-TOF MS. El 88,2% fueron identificados como Moraxella lacunata y el 11,8% como Moraxella nonliquefaciens. La subtipificación molecular se realizó por la técnica de electroforesis en gel de campo pulsado (PFGE). Todos los aislamientos fueron tipificables y se identificaron 13 patrones de digestión. Nuestros resultados muestran que la técnica de PFGE con la enzima SmaI es útil para hacer estudios epidemiológicos en cepas de estas especies.

9.
Rev Argent Microbiol ; 55(2): 160-166, 2023.
Article in Spanish | MEDLINE | ID: mdl-36604301

ABSTRACT

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.


Subject(s)
Legionella pneumophila , Legionnaires' Disease , Humans , Legionnaires' Disease/diagnosis , Legionnaires' Disease/epidemiology , Legionnaires' Disease/urine , Argentina/epidemiology , Legionella pneumophila/genetics , Polymerase Chain Reaction/methods , DNA
10.
Rev Argent Microbiol ; 55(1): 20-24, 2023.
Article in English | MEDLINE | ID: mdl-35915013

ABSTRACT

This is the first study of the genetic diversity of Moraxella spp. Isolates were detected in an Eye Hospital in the City of Buenos Aires. Due to the high frequency of Moraxella spp. observed in corneal abscesses, we decided to validate their identification at the species level, determine their drug susceptibility and perform molecular subtyping. Seventeen (17) isolates obtained from corneal abscesses were evaluated. The identification was carried out using a combination of biochemical tests and MALDI-TOF mass spectrometry. Of these isolates, 88.2% were identified as Moraxella lacunata, and 11.8% as Moraxella nonliquefaciens. Molecular subtyping was performed using the pulsed-field gel electrophoresis (PFGE) technique. All isolates were typable and thirteen digestion patterns were identified. Based on the obtained results, the PFGE technique using the SmaI enzyme can be used for epidemiological studies of strains of these species.


Subject(s)
Abscess , Moraxella , Humans , Moraxella/genetics , Electrophoresis, Gel, Pulsed-Field , Genetic Variation
11.
Sci Rep ; 12(1): 11469, 2022 07 06.
Article in English | MEDLINE | ID: mdl-35794460

ABSTRACT

Sepsis has been called the graveyard of pharmaceutical companies due to the numerous failed clinical trials. The lack of tools to monitor the immunological status in sepsis constrains the development of therapies. Here, we evaluated a test based on whole plasma peptidome acquired by MALDI-TOF-mass spectrometer and machine-learning algorithms to discriminate two lipopolysaccharide-(LPS) induced murine models emulating the pro- and anti-inflammatory/immunosuppression environments that can be found during sepsis. The LPS group was inoculated with a single high dose of LPS and the IS group was subjected to increasing doses of LPS, to induce proinflammatory and anti-inflammatory/immunosuppression profiles respectively. The LPS group showed leukopenia and higher levels of cytokines and tissue damage markers, and the IS group showed neutrophilia, lymphopenia and decreased humoral response. Principal component analysis of the plasma peptidomes formed discrete clusters that mostly coincided with the experimental groups. In addition, machine-learning algorithms discriminated the different experimental groups with a sensitivity of 95.7% and specificity of 90.9%. Data reveal the potential of plasma fingerprints analysis by MALDI-TOF-mass spectrometry as a simple, speedy and readily transferrable method for sepsis patient stratification that would contribute to therapeutic decision-making based on their immunological status.


Subject(s)
Lipopolysaccharides , Sepsis , Animals , Cytokines , Humans , Leukocyte Count , Mice , Proof of Concept Study
12.
J Infect Dev Ctries ; 16(5): 835-842, 2022 05 30.
Article in English | MEDLINE | ID: mdl-35656955

ABSTRACT

INTRODUCTION: The Burkholderia cepacia complex (BCC) bacteria are opportunistic pathogens that cause nosocomial infections and are especially dangerous for cystic fibrosis (CF) patients. Burkholderia contaminans is an emerging BCC species isolated from CF patients that also occurs as a contaminant in pharmaceutical and personal care products, sometimes linking it with outbreaks. METHODOLOGY: A total of 55 B. contaminans isolates from CF and non-CF patients in Argentina were identified by recA sequencing and MALDI TOF MS. A standardized Pulsed Field Gel Electrophoresis (PFGE) protocol was set up in order to assess genetic diversity, outbreak investigations, and possible clone persistence. RESULTS: All isolates were identified as B. contaminans by both MALDI-TOF MS and recA sequence analysis. PFGE has enabled us to compare and determine the genetic relationship between B. contaminans isolates. Isolates were distributed in different PFGE clusters with evidence of the presence and persistence of a clone, over a period of 3 years, in the same hospital. This large hospital outbreak involved CF and non-CF patients. Moreover, PFGE results showed a good correlation between sporadic or outbreak-related isolates and the available epidemiological information. CONCLUSIONS: These findings highlight the importance of B. contaminans in Argentina and provide evidence for encouraging the surveillance of highly transmissible clones. The study also contributes to global knowledge about B. contaminans infections.


Subject(s)
Burkholderia Infections , Burkholderia cepacia complex , Cystic Fibrosis , Argentina/epidemiology , Burkholderia , Burkholderia Infections/epidemiology , Burkholderia Infections/microbiology , Burkholderia cepacia complex/genetics , Cystic Fibrosis/complications , Humans
13.
Rev. argent. microbiol ; Rev. argent. microbiol;54(2): 111-120, jun. 2022. graf
Article in Spanish | LILACS-Express | LILACS | ID: biblio-1407186

ABSTRACT

Resumen Actinotignum schaalii es un patógeno emergente en pacientes ancianos con patologías del tracto urinario. Se describen dos casos de bacteriemias por A. schaalii. Caso 1: Paciente de 79 años, con antecedente de hiperplasia benigna prostética. Ingresó a la guardia por síndrome febril, dolor abdominal y disuria. Caso 2: Paciente de 95 anos con adenomectomía prostética, uretrostomía por estrechez uretral e hiperplasia benigna prostética. Ingresó por síndrome febril, tos productiva, infiltrados bilaterales con imagen paracardíaca derecha y derrame pleural. En ambos pacientes se aisló A. schaalii en hemocultivos, identificado por espectrometría de masas MALDI-TOF MS. Solo en el caso 1 se confirmó que el foco de la bacteriemia fue urinario. Es importante sospechar la presencia de este patógeno emergente en infecciones urinarias con sedimento patológico, sin desarrollo en medios de cultivo tradicionales, para garantizar un tratamiento empírico adecuado, ya que la mayoría de los aislamientos presentan resistencia a ciprofloxacina y trimetoprima-sulfametoxazol.


Abstract Actinotignum schaalii is an emerging pathogen in elderly patients with urinary tract pathologies. Two cases of A. schaalii bacteremia are described. Case 1: 79-year-old patient with a history of benign prostatic hyperplasia. He was admitted to the ward for febrile syn-drome, abdominal pain, and dysuria. Case 2: 95-year-old patient with prostatic adenomectomy, urethrostomy due to urethral stricture, and benign prostatic hyperplasia. He was admitted due to febrile syndrome, productive cough, bilateral infiltrates with right paracardiac image, and pleural effusion. In both patients, A. schaalii was isolated in blood cultures, identified by MALDITOF-MS mass spectrometry. Only in case 1 was it confirmed that the focus of bac-teremia was urinary. It is important to suspect this emerging pathogen in urinary infections with pathological sediment without developing in traditional culture media to ensure ade-quate empirical treatment. Since most of the isolates show resistance to ciprofloxacin and trimethoprim-sulfamethoxazole.

14.
Rev Argent Microbiol ; 54(2): 110-113, 2022.
Article in Spanish | MEDLINE | ID: mdl-34903428

ABSTRACT

Actinotignum schaalii is an emerging pathogen in elderly patients with urinary tract pathologies. Two cases of A. schaalii bacteremia are described. Case 1: 79-year-old patient with a history of benign prostatic hyperplasia. He was admitted to the ward for febrile syndrome, abdominal pain, and dysuria. Case 2: 95-year-old patient with prostatic adenomectomy, urethrostomy due to urethral stricture, and benign prostatic hyperplasia. He was admitted due to febrile syndrome, productive cough, bilateral infiltrates with right paracardiac image, and pleural effusion. In both patients, A. schaalii was isolated in blood cultures, identified by MALDITOF-MS mass spectrometry. Only in case 1 was it confirmed that the focus of bacteremia was urinary. It is important to suspect this emerging pathogen in urinary infections with pathological sediment without developing in traditional culture media to ensure adequate empirical treatment. Since most of the isolates show resistance to ciprofloxacin and trimethoprim-sulfamethoxazole.


Subject(s)
Actinomycetaceae , Bacteremia , Prostatic Hyperplasia , Urinary Tract Infections , Aged , Aged, 80 and over , Argentina , Humans , Male
15.
Sensors (Basel) ; 21(20)2021 Oct 09.
Article in English | MEDLINE | ID: mdl-34695923

ABSTRACT

Cities have high demand and limited availability of water and energy, so it is necessary to have adequate technologies to make efficient use of these resources and to be able to generate them. This research focuses on developing and executing a methodology for an urban living lab vocation identification for a new water and energy self-sufficient university building. The methods employed were constructing a technological roadmap to identify global trends and select the technologies and practices to be implemented in the building. Among the chosen technologies were those for capturing and using rain and residual water, the generation of solar energy, and water and energy generation and consumption monitoring. This building works as a living laboratory since the operation and monitoring generate knowledge and innovation through students and research groups that develop projects. The insights gained from this study may help other efforts to avoid pitfalls and better design smart living labs and off-grid buildings.


Subject(s)
Rain , Universities , Cities , Humans , Technology , Water
17.
J Virol Methods ; 286: 113991, 2020 12.
Article in English | MEDLINE | ID: mdl-33045283

ABSTRACT

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.


Subject(s)
Betacoronavirus/isolation & purification , Clinical Laboratory Techniques/methods , Coronavirus Infections/diagnosis , Nasopharynx/virology , Pneumonia, Viral/virology , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , COVID-19 , COVID-19 Testing , COVID-19 Vaccines , Coronavirus Infections/virology , Humans , Machine Learning , Mass Screening/methods , Multivariate Analysis , Pandemics , Pneumonia, Viral/diagnosis , Real-Time Polymerase Chain Reaction , SARS-CoV-2 , Sensitivity and Specificity
18.
Rev Panam Salud Publica ; 44, sept. 2020
Article in Spanish | PAHO-IRIS | ID: phr-52282

ABSTRACT

[RESUMEN]. Objetivo. El objetivo es presentar los resultados del Programa Latinoamericano de Aseguramiento de la Calidad en Bacteriología y Resistencia a los Antimicrobianos (LA-EQAS) entre 2000 y 2018 y la evolución en la detección de mecanismos de resistencia de impacto clínico. Métodos. Los Laboratorios Nacionales de Referencia (LNR) participantes recibieron 25 encuestas con 10 cepas cada una, representando un total de 86 especies bacterianas y 40 mecanismos de resistencia. Para evaluar el desempeño de los LNR, se analizaron cinco indicadores: identificación bacteriana, interpretación de las pruebas de sensibilidad, rangos de las zonas de inhibición aceptables, mecanismo de resistencia inferido, y tiempo de demora en la respuesta. Resultados. La concordancia media fue 82,6% (rango: 74-95%) en la identificación bacteriana, 93,3% (85-98%) en la interpretación de las pruebas de sensibilidad, 84,6% (70-94%) en las zonas de inhibición, 82,5% (73-96%) en el mecanismo de resistencia inferido, y la demora en la respuesta, 34 días. Se observó una mejora en la detección de mecanismos de relevancia clínica como resistencia a meticilina, macrólidos y glucopéptidos en cocos gram positivos, y betalactamasas de espectro extendido, AmpC plasmídico y carbapenemasas en bacilos gram negativos. Conclusiones. El LA-EQAS es una excelente herramienta para la mejora continua de la calidad en el diagnóstico de las infecciones por microorganismos multirresistentes en los LNR de América Latina.


[RESUMEN]. Objetivo. El objetivo es presentar los resultados del Programa Latinoamericano de Aseguramiento de la Calidad en Bacteriología y Resistencia a los Antimicrobianos (LA-EQAS) entre 2000 y 2018 y la evolución en la detección de mecanismos de resistencia de impacto clínico. Métodos. Los Laboratorios Nacionales de Referencia (LNR) participantes recibieron 25 encuestas con 10 cepas cada una, representando un total de 86 especies bacterianas y 40 mecanismos de resistencia. Para evaluar el desempeño de los LNR, se analizaron cinco indicadores: identificación bacteriana, interpretación de las pruebas de sensibilidad, rangos de las zonas de inhibición aceptables, mecanismo de resistencia inferido, y tiempo de demora en la respuesta. Resultados. La concordancia media fue 82,6% (rango: 74-95%) en la identificación bacteriana, 93,3% (85-98%) en la interpretación de las pruebas de sensibilidad, 84,6% (70-94%) en las zonas de inhibición, 82,5% (73-96%) en el mecanismo de resistencia inferido, y la demora en la respuesta, 34 días. Se observó una mejora en la detección de mecanismos de relevancia clínica como resistencia a meticilina, macrólidos y glucopéptidos en cocos gram positivos, y betalactamasas de espectro extendido, AmpC plasmídico y carbapenemasas en bacilos gram negativos. Conclusiones. El LA-EQAS es una excelente herramienta para la mejora continua de la calidad en el diagnóstico de las infecciones por microorganismos multirresistentes en los LNR de América Latina.


[RESUMO]. Objetivo. O objetivo deste trabalho é apresentar os resultados do Programa Latino-Americano de Garantia da Qualidade em Bacteriologia e Resistência Antimicrobiana (LA-EQAS, na sigla em inglês) entre 2000 e 2018 e a evolução na detecção de mecanismos de resistência com impacto clínico. Métodos. Os Laboratórios Nacionais de Referência (LNRs) participantes receberam 25 inquéritos com 10 cepas bacterianas cada, representando um total de 86 espécies bacterianas e 40 mecanismos de resistência. Para avaliar o desempenho dos LNRs, foram analisados cinco indicadores: identificação bacteriana, interpretação dos testes de sensibilidade, faixas das zonas de inibição aceitáveis, mecanismo de resistência inferido e tempo de demora na resposta. Resultados. A concordância média foi de 82,6% (intervalo: 74-95%) na identificação bacteriana, 93,3% (85-98%) na interpretação dos testes de sensibilidade, 84,6% (70-94%) nas zonas de inibição, 82,5% (73-96%) no mecanismo de resistência inferido e 34 dias na demora na resposta. Observou-se uma melhoria na detecção de mecanismos clinicamente relevantes, como a resistência a meticilina, macrolídeos e glicopeptídeos em cocos Gram-positivos, beta-lactamases de espectro ampliado, AmpC plasmídica e carbapenemases em bacilos Gram-negativos. Conclusões. O LA-EQAS é uma excelente ferramenta para a melhoria contínua da qualidade no diagnóstico de infecções por microrganismos multirresistentes nos LNRs da América Latina.


Subject(s)
Anti-Infective Agents , Surveillance in Disasters , Quality Control , Bacteriology , Latin America , Anti-Infective Agents , Surveillance in Disasters , Quality Control , Bacteriology , Latin America , Anti-Infective Agents , Surveillance in Disasters , Quality Control
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