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1. Metagenomic analysis reveals differences in the co-occurrence and abundance of viral species in SARS-CoV-2 patients with different severity of disease

Author

Pavel Iša, Blanca Taboada, Rodrigo García-López, Celia Boukadida, José Ernesto Ramírez-González, Joel Armando Vázquez-Pérez, Alejandra Hernández-Terán, José Ángel Romero-Espinoza, José Esteban Muñoz-Medina, Concepción Grajales-Muñiz, Alma Rincón-Rubio, Margarita Matías-Florentino, Alejandro Sanchez-Flores, Edgar Mendieta-Condado, Gisela Barrera-Badillo, Susana López, Lucía Hernández-Rivas, Irma López-Martínez, Santiago Ávila-Ríos, and Carlos F. Arias

Subjects
SARS-CoV-2, Respiratory viruses, Metagenomic sequencing, COVID-19, Disease severity, Infectious and parasitic diseases, RC109-216
Abstract

Abstract Background SARS-CoV-2 infections have a wide spectrum of clinical manifestations whose causes are not completely understood. Some human conditions predispose to severe outcome, like old age or the presence of comorbidities, but many other facets, including coinfections with other viruses, remain poorly characterized. Methods In this study, the eukaryotic fraction of the respiratory virome of 120 COVID-19 patients was characterized through whole metagenomic sequencing. Results Genetic material from respiratory viruses was detected in 25% of all samples, whereas human viruses other than SARS-CoV-2 were found in 80% of them. Samples from hospitalized and deceased patients presented a higher prevalence of different viruses when compared to ambulatory individuals. Small circular DNA viruses from the Anneloviridae (Torque teno midi virus 8, TTV-like mini virus 19 and 26) and Cycloviridae families (Human associated cyclovirus 10), Human betaherpesvirus 6, were found to be significantly more abundant in samples from deceased and hospitalized patients compared to samples from ambulatory individuals. Similarly, Rotavirus A, Measles morbillivirus and Alphapapilomavirus 10 were significantly more prevalent in deceased patients compared to hospitalized and ambulatory individuals. Conclusions Results show the suitability of using metagenomics to characterize a broader peripheric virological landscape of the eukaryotic virome in SARS-CoV-2 infected patients with distinct disease outcomes. Identified prevalent viruses in hospitalized and deceased patients may prove important for the targeted exploration of coinfections that may impact prognosis.

Published
2022
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2. Genomic Characterization of SARS-CoV-2 Isolated from Patients with Distinct Disease Outcomes in Mexico

Author

Celia Boukadida, Blanca Taboada, Marina Escalera-Zamudio, Pavel Isa, José Ernesto Ramírez-González, Joel Armando Vazquez-Perez, José Esteban Muñoz-Medina, Concepción Grajales-Muñiz, Carolina González-Torres, Francisco Javier Gaytán-Cervantes, Alma Rincón-Rubio, Margarita Matías-Florentino, Héctor Esteban Paz-Juárez, Alejandro Sanchez-Flores, Edgar Mendieta-Condado, Gisela Barrera-Badillo, Lucía Hernández-Rivas, Susana López, Irma López-Martínez, Santiago Ávila-Ríos, and Carlos F. Arias

Subjects
SARS-CoV-2, genomic diversity, Mexico, distinct clinical outcomes, Microbiology, QR1-502
Abstract

ABSTRACT The coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has shown a wide spectrum of clinical manifestations ranging from asymptomatic infections to severe disease and death. Pre-existing medical conditions and age have been mainly linked to the development of severe disease; however, the potential association of viral genetic characteristics with different clinical conditions remains unclear. SARS-CoV-2 variants with increased transmissibility were detected early in the pandemics, and several variants with potential relevance for public health are currently circulating around the world. In this study, we characterized 57 complete SARS-CoV-2 genomes during the exponential growth phase of the early epidemiological curve in Mexico, in April 2020. Patients were categorized under distinct disease severity outcomes: mild disease or ambulatory care, severe disease or hospitalized, and deceased. To reduce bias related to risk factors, the patients were less than 60 years old and with no diagnosed comorbidities A trait-association phylogenomic approach was used to explore genotype–phenotype associations, represented by the co-occurrence of mutations, disease severity outcome categories, and clusters of Mexican sequences. Phylogenetic results revealed a higher genomic diversity compared to the initial viruses detected during the early stage of the local epidemic. We identified a total of 90 single nucleotide variants compared to the Wuhan-Hu-1 genome, including 54 nonsynonymous mutations. We did not find evidence for the co-occurrence of mutations associated with specific disease outcomes. Therefore, in the group of patients studied, disease severity was likely mainly driven by the host genetic background and other demographic factors. IMPORTANCE The genetic association of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) with different clinical conditions remains unclear and needs further investigation. In this study, we characterized 57 complete SARS-CoV-2 genomes from patients in Mexico with distinct disease severity outcomes: mild disease or ambulatory care, severe disease or hospitalized, and deceased. To reduce bias related to risk factors the patients were less than 60 years old and with no diagnosed comorbidities. We did not find evidence for the co-occurrence of mutations associated with specific disease outcomes. Therefore, in the group of patients studied, disease severity was likely mainly driven by the host genetic background and other demographic factors.

Published
2022
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3. Genetic Analysis of SARS-CoV-2 Variants in Mexico during the First Year of the COVID-19 Pandemic

Author

Blanca Taboada, Selene Zárate, Pavel Iša, Celia Boukadida, Joel Armando Vazquez-Perez, José Esteban Muñoz-Medina, José Ernesto Ramírez-González, Andreu Comas-García, Concepción Grajales-Muñiz, Alma Rincón-Rubio, Margarita Matías-Florentino, Alejandro Sanchez-Flores, Edgar Mendieta-Condado, Jerome Verleyen, Gisela Barrera-Badillo, Lucía Hernández-Rivas, Fidencio Mejía-Nepomuceno, José Arturo Martínez-Orozco, Eduardo Becerril-Vargas, Susana López, Irma López-Martínez, Santiago Ávila-Ríos, and Carlos F. Arias

Subjects
viral diversity, SARS-CoV-2, genomic surveillance, Microbiology, QR1-502
Abstract

During the first year of the SARS-CoV-2 pandemic in Mexico, more than two million people were infected. In this study, we analyzed full genome sequences from 27 February 2020 to 28 February 2021 to characterize the geographical and temporal distribution of SARS-CoV-2 lineages and identify the most common circulating lineages during this period. We defined six different geographical regions with particular dynamics of lineage circulation. The Northeast and Northwest regions were the ones that exhibited the highest lineage diversity, while the Central south and South/Southeast regions presented less diversity with predominance of a certain lineage. Additionally, by late February 2021, lineage B.1.1.519 represented more than 89% of all circulating lineages in the country.

Published
2021
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5. Detección del primer caso de COVID-19 relacionado a la variante Ómicron en México

Author

Armando Rojo Enríquez, Pilar Escamilla Llano, Raymundo Rodríguez Sandoval, Leonardo Medina Arias, Miriam Ixchel García Franco, Leticia Ramírez De La O, Irma López Martínez, Claudia Wong Arámbula, Abril Rodríguez Maldonado, Vanessa Rivero Arredondo, Ariadna Medina Benítez, Joaquín Quiroz Mercado, Maribel González Villa, Natividad Cruz Ortiz, Tatiana Núñez García, Gisela Barrera Badillo, Fernando González Domínguez, Lucía Hernández Rivas, and Ernesto Ramírez González

Subjects
General Materials Science
Published
2022

6. Draft genome sequence of first Vibrio diabolicus in Mexico strain InDRE-D1-M1, an emergent threat

Author

Elena Berenice Nava-Soberanes, Edgar Ruben Mendieta-Condado, Fabiola Garcés-Ayala, Adnan Araiza-Rodríguez, Pablo Aguilera-Perez, Alberto Alfaro-López, Alma Cecilia Ibarra-Buelna, Norma Angélica Montes-Colima, Irma López-Martínez, Lucía Hernández-Rivas, Afonso Méndez-Tenorio, Maribel González-Villa, Jorge Membrillo-Hernandez, José Ernesto Ramírez-González, and Alma Guadalupe Buelna-Romero

Subjects
DNA, Bacterial, Infectious Diseases, Virology, Drug Resistance, Bacterial, Parasitology, Sequence Analysis, DNA, General Medicine, Mexico, Microbiology, Multilocus Sequence Typing, Vibrio
Abstract

Introduction: The complete genome of the marine environmental bacterium Vibrio diabolicus isolated from raw shrimp in the city of Guadalajara in the state of Jalisco in Mexico is reported here. Methodology: Vibrio spp. it was isolated and identified using standard microbiological and molecular techniques. Whole genome sequencing was performed using the Miseq system (Illumina, USA). Results: The Multi Locus Sequence Typing profile of the isolated Vibrio bacteria coincided only with 4 specific loci (atpA, gyrB, pyrH and recA) and with a total coverage of the species belonging to Vibrio spp. Analysis of the complete genome of the Vibrio isolate and other closely related species, using the genomic fingerprints of the Virtual Analysis Method for PHylogenomic fingerprint estimation (VAMPHyRe) software, revealed the clustering of this species among the clade Vibrio diabolicus. The antibiogram revealed that this strain of Vibrio diabolicus is resistant to ampicillin, which is consistent with the bioinformatic finding of the β-lactamase enzyme that hydrolyzes carbenicillin class A. Conclusions: This study demonstrated that the environmental marine bacterium Vibrio diabolicus contains carrier genes associated with pathogenicity and ecological function, which could represent a threat to public health.

Published
2021

7. Emergence and spread of the potential variant of interest (VOI) B.1.1.519 of SARS-CoV-2 predominantly present in Mexico

Author

Dulibeth Gonzalez-Barrera, Tatiana Ernestina Nuñez-García, Alejandro Sanchez-Flores, Juan Pablo Reyes-Grajeda, Eduardo Becerril-Vargas, Daniel Rangel-DeLeon, Alejandra Hernández-Terán, Fernando Penaloza-Figueroa, Fidencio Mejía-Nepomuceno, Margarita Matías-Florentino, Rogelio Pérez-Padilla, Joel A. Vazquez-Perez, Pavel Isa, Abril Paulina Rodríguez-Maldonado, Santiago Ávila-Ríos, Concepción Grajales-Muñiz, Nicolas Alcaraz, Angel Gustavo Salas-Lais, Luis Alonso Herrera-Montalvo, Mario Mujica-Sanchez, Alfredo Mendoza-Vargas, Claudia Wong-Arámbula, Irma López-Martínez, José Arturo Martínez-Orozco, Celia Boukadida, Blanca Taboada, Andrea Santos Coy-Arechavaleta, José Ernesto Ramírez-González, José Esteban Muñoz-Medina, Jorge Salas-Hernández, Lucía Hernández-Rivas, Alfredo Hidalgo-Miranda, Gisela Barrera-Badillo, Alberto Cedro-Tanda, Carlos F. Arias, and Natividad Cruz-Ortiz

Subjects
Mutation, 2019-20 coronavirus outbreak, Lineage (genetic), SARS-CoV-2, Brief Report, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), COVID-19, Spike Protein, Genome, Viral, General Medicine, Biology, medicine.disease_cause, Virology, Virus, First trimester, Phylogenetics, Spike Glycoprotein, Coronavirus, Prevalence, medicine, Humans, Mexico, Phylogeny
Abstract

SARS-CoV-2 variants emerged in late 2020, and at least three variants of concern (B.1.1.7, B.1.351, and P1) have been reported by WHO. These variants have several substitutions in the spike protein that affect receptor binding; they exhibit increased transmissibility and may be associated with reduced vaccine effectiveness. In the present work, we report the identification of a potential variant of interest, harboring the mutations T478K, P681H, and T732A in the spike protein, within the newly named lineage B.1.1.519, that rapidly outcompeted the preexisting variants in Mexico and has been the dominant virus in the country during the first trimester of 2021.

Published
2021

8. Full genome sequence of the first SARS-CoV-2 detected in Mexico

Author

Lourdes Lloret-Sánchez, Tatiana Ernestina Nuñez-García, Eduardo Becerril-Vargas, Fabiola Garcés-Ayala, Juan Carlos del Mazo-López, Maribel González-Villa, Magaly Guadalupe Landa-Flores, Miguel Ángel Fierro-Valdez, Daniel Regalado-Santiago, Gisela Barrera-Badillo, Edgar Mendieta-Condado, Natividad Cruz-Ortiz, Nancy Martínez-Velázquez, Hugo López-Gatell, Adnan Araiza-Rodríguez, Abril Paulina Rodríguez-Maldonado, Joel A. Vazquez-Perez, Lucía Hernández-Rivas, Irma López-Martínez, David Esaú Fragoso-Fonseca, José Luis Alomía-Zegarra, Adriana Ruiz-López, María del Carmen Esteban-Valencia, Jorge Salas, Noé Escobar-Escamilla, Mireya Mederos-Michel, Nervain Benjamin Contreras-González, José Ernesto Ramírez-González, Dayanira Sarith Arellano-Suarez, Claudia Wong-Arámbula, and José Arturo Martínez-Orozco

Subjects
Adult, Male, Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Lineage (evolution), Pneumonia, Viral, Genome, Viral, Biology, 03 medical and health sciences, Betacoronavirus, Phylogenetics, Annotated Sequence Record, Virology, Humans, Base sequence, Mexico, Pandemics, Phylogeny, 030304 developmental biology, Genetics, Whole genome sequencing, 0303 health sciences, Phylogenetic tree, Base Sequence, Whole Genome Sequencing, 030306 microbiology, SARS-CoV-2, COVID-19, Subclade, General Medicine, Coronavirus Infections
Abstract

SARS-CoV-2 was first detected in the city of Wuhan, Hubei Province, China. In this report, we describe the complete genome sequence of the first imported SARS-CoV-2, detected in a Mexican patient who had traveled to Bergamo, Italy. Phylogenetic analysis showed that this isolate belongs to subclade A2a (lineage G) and is closely related to isolates from Finland, Germany and Brazil, all of which were from patients with a history of travel to Italy. This is the first report of the complete genome sequence of this virus in Mexico.

Published
2020

9. Complete genome sequence of a coxsackievirus type A24 variant causing an outbreak of acute haemorrhagic conjunctivitis in southeastern Mexico in 2017

Author

Fabiola Garcés-Ayala, Lucía Hernández-Rivas, David Esaú Fragoso-Fonseca, Edgar Mendieta-Condado, Noé Escobar-Escamilla, José Ernesto Ramírez-González, Elizabeth González-Durán, Irma López-Martínez, Fernando I. Puerto, Gisela Barrera-Badillo, José Alberto Díaz-Quiñonez, and Abril Paulina Rodríguez-Maldonado

Subjects
medicine.medical_specialty, Coxsackievirus Infections, Genome, Viral, Coxsackievirus, Genome, Virus, Disease Outbreaks, 03 medical and health sciences, Medical microbiology, Virology, Genotype, medicine, Humans, Clade, Mexico, 030304 developmental biology, Whole genome sequencing, 0303 health sciences, Base Sequence, Whole Genome Sequencing, biology, 030306 microbiology, Outbreak, General Medicine, biology.organism_classification, Enterovirus C, Human, Conjunctivitis, Acute Hemorrhagic
Abstract

Cases of acute haemorrhagic conjunctivitis (AHC) caused by a coxsackie virus A24 variant (CV-A24v) in Mexico have been reported since 1987; however, no molecular data on the causative strains have been available. Here, we report the identification of the etiological agent responsible for the most recent AHC outbreak in southeastern Mexico (at the end of 2017) as well as the complete genome sequences of seven isolates, using next-generation sequencing (NGS). Phylogenomic analysis of the CV-A24v sequences reported here showed similarity to contemporary strains causing AHC outbreaks in French Guiana and Uganda, forming a novel clade related to genotype IV. Moreover, a specific mutational pattern in the non-structural proteins was identified in the 2017 isolates. This is the first report of genetic characterization of CV-A24v isolates obtained in Mexico.

Published
2020

10. Respiratory syncytial virus outbreak DURING THE COVID-19 PANDEMIC. How has it changed?

Author

Lucía Hernández-Rivas, Teresa Pedraz, Cristina Calvo, Isabel San Juan, M.ª José Mellado, and Ana Robustillo

Subjects
Microbiology (medical), children, COVID-19 pandemic, Pandemia COVID-19, epidemiology, syncytial respiratory virus, virus respiratorio sincitial, Article, niños, epidemiología
Abstract

Introducción: La epidemiología de la infección por virus respiratorio sincitial (VRS) ha cambiado durante la pandemia de COVID-19. Nuestros objetivos fueron describir la epidemia de VRS en 2021 y compararla con los años previos a la pandemia. Métodos: estudio retrospectivo realizado en Madrid (España) en un hospital pediátrico terciario comparando los datos epidemiológicos y clínicos de los ingresos por VRS durante 2021 y las dos temporadas anteriores. Resultados: 899 niños ingresaron por infección por VRS en el período de estudio. Durante 2021, el brote alcanzó su punto máximo en junio y los últimos casos se identificaron en julio. Las temporadas anteriores se detectaron en otoño-invierno. El número de hospitalizaciones en 2021 fue significativamente menor que en temporadas anteriores. No hubo diferencias entre temporadas en cuanto a edad, sexo o gravedad de la enfermedad. Conclusión: Las hospitalizaciones por VRS durante 2021 en España se trasladaron a verano sin casos en otoño e invierno 2020-2021. A diferencia de otros países, los datos clínicos fueron similares entre epidemias.

Published
2021

11. Genetic Analysis of SARS-CoV-2 Variants in Mexico during the First Year of the COVID-19 Pandemic

Author

Susana López, José Esteban Muñoz-Medina, Blanca Taboada, Gisela Barrera-Badillo, Concepción Grajales-Muñiz, Irma López-Martínez, Margarita Matías-Florentino, Pavel Isa, José Arturo Martínez-Orozco, Lucía Hernández-Rivas, José Ernesto Ramírez-González, Alma Rincón-Rubio, Joel A. Vazquez-Perez, Selene Zárate, Edgar Mendieta-Condado, Celia Boukadida, Jerome Verleyen, Eduardo Becerril-Vargas, Santiago Ávila-Ríos, Fidencio Mejía-Nepomuceno, Alejandro Sanchez-Flores, Andreu Comas-García, and Carlos F. Arias

Subjects
Coronavirus disease 2019 (COVID-19), Whole Genome Sequencing, SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Lineage (evolution), COVID-19, Genetic Variation, Genome, Viral, Biology, Genetic analysis, Genome, Microbiology, QR1-502, Article, genomic surveillance, Evolution, Molecular, Infectious Diseases, viral diversity, Evolutionary biology, Virology, Pandemic, Humans, Genetic Testing, Mexico, Phylogeny
Abstract

During the first year of the SARS-CoV-2 pandemic in Mexico, more than two million people were infected. In this study, we analyzed full genome sequences from 27 February 2020 to 28 February 2021 to characterize the geographical and temporal distribution of SARS-CoV-2 lineages and identify the most common circulating lineages during this period. We defined six different geographical regions with particular dynamics of lineage circulation. The Northeast and Northwest regions were the ones that exhibited the highest lineage diversity, while the Central south and South/Southeast regions presented less diversity with predominance of a certain lineage. Additionally, by late February 2021, lineage B.1.1.519 represented more than 89% of all circulating lineages in the country.

Published
2021

12. Emergence and spread of the potential variant of interest (VOI) B.1.1.519 predominantly present in Mexico

Author

Juan Pablo Reyes-Grajeda, Fernando Penaloza-Figueroa, Luis Alonso Herrera-Montalvo, Dulibeth Gonzalez-Barrera, Tatiana Ernestina Nuñez-García, Alfredo Mendoza-Vargas, Alberto Cedro-Tanda, Alejandro Sanchez-Flores, José Esteban Muñoz-Medina, Jorge Salas-Hernández, Natividad Cruz-Ortiz, Gisela Barrera-Badillo, Blanca Taboada, Alfredo Hidalgo-Miranda, Abril Paulina Rodríguez-Maldonado, Lucía Hernández-Rivas, Santiago Ávila-Ríos, Concepción Grajales-Muñiz, Nicolas Alcaraz, Irma López-Martínez, Margarita Matías-Florentino, Joel A. Vazquez-Perez, Fidencio Mejía-Nepomuceno, José Ernesto Ramírez-González, Mario Mujica-Sanchez, Celia Boukadida, Alejandra Hernández-Terán, Carlos F. Arias, Rogelio Pérez-Padilla, Pavel Isa, Daniel Rangel-DeLeon, Eduardo Becerril-Vargas, Angel Gustavo Salas-Lais, Andrea Santos Coy-Arechavaleta, Claudia Wong-Arámbula, and José Arturo Martínez-Orozco

Subjects
Genetics, First trimester, 2019-20 coronavirus outbreak, Lineage (genetic), Coronavirus disease 2019 (COVID-19), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Spike Protein, Biology, Virus
Abstract

SARS-CoV-2 variants have emerged in late 2020 and there are at least three variants of concern (B.1.1.7, B.1.351, P1) reported by WHO. These variants have several substitutions in the Spike protein that affect receptor binding; they present increased transmissibility and may be associated with reduced vaccine effectiveness. In the present work, we are reporting the identification of a potential variant of interest harboring the mutations T478K, P681H, and T732A in the Spike protein, within the newly named lineage B.1.1.519, which rapidly outcompeted the preexisting variants in Mexico and has been the dominant virus in the country during the first trimester of 2021.

Published
2021

13. Development and validation of a prediction model for 30-day mortality in hospitalised patients with COVID-19: the COVID-19 SEIMC score

Author

Juan Salillas, Miguel Fernández Huerta, Patricio González-Pizarro, Francisco Javier Membrillo, Raul Galera, Jesús Rodríguez-Baño, Lydia Galvez, Juan Cuadros-González, Aina Gabarrell-Pascuet, Jorge Diaz-Garzon, INMA JARRIN, Claudia González-Rico, Alicia Rico Nieto, Cristina Cervera, Carlos Bea Serrano, Alberto Ouro Villasante, Guillermo Ruiz-Carrascoso, Beatriz Díaz-Pollán, María del mar Arcos Rueda, Julio Garcia-Rodriguez, BELEN GUTIÉRREZ-GUTIÉRREZ, MARCO ANTONIO SEMPERE ALCOCER, Cristina Verdú Sánchez, Lucía Hernández-Rivas, Guillermo Cuervo, Alejandro Smithson, Miguel Torralba, Iván Bloise, Alexander Rombauts, Carlos Toro, Lucio Jesus García-Fraile Fraile, Alejandro García-Ruiz de Morales, Cecilia Tortajada, KAPIL LAXMAN NANWANI NANWANI, Lorena De la Mora Cañizo, Laia Lorenzo-Esteller, Jorge Álvarez Troncoso, Cristina Roca Oporto, Alejandro Martin-Quiros, José A. Oteo, Eduardo Malmierca Corral, Stefan Stewart, Jerónimo Pachón, Almudena Gutiérrez-Arroyo, Moreno-Cuerda Victor, Carlos Carpio, Emilio Cendejas-Bueno, Pilar Fernandez-Calle, Antonio Javier Carcas Sansuán, Alexy Inciarte, Pablo Ryan, Luis Puente-Maestu, Jesús Troya García, Francisco de Asís Alcántara Nicolás, Gabriela Abelenda-Alonso, Natividad Benito, Daniel Prieto Arribas, Jesus Mingorance, Jose L Del Pozo, Jordi Carratala, Cristina Marcelo, Marta Ruiz-Algueró, Sarah CARO BRAGADO, Juan Berenguer, Vicens Diaz-Brito, Víctor Hontañón Antoñana, Julen Cadiñanos, Jose Arribas, María Jesús Jaras Hernández, Henar Calvo Sánchez, Elisa Cordero, Instituto de Salud Carlos III, Fundación Seimc-Gesida, Plan Nacional de I+D+i (España), Ministerio de Ciencia y Universidades (España), Unión Europea. Fondo Europeo de Desarrollo Regional (FEDER/ERDF), Red de Investigación Cooperativa en Investigación en Sida (España), Red de Investigación Cooperativa en Investigación en Patología Infecciosa (España), Fundación SEIMC-GESIDA, Ministerio de Ciencia, Innovación y Universidades (España), European Commission, Red Española de Investigación en SIDA, Red Española de Investigación en Patología Infecciosa, Universidad de Cantabria, UAM. Departamento de Farmacología, and UAM. Departamento de Medicina

Subjects
Male, Neutrophils, Respiratory Infection, 030204 cardiovascular system & hematology, Logistic regression, 0302 clinical medicine, Diagnòstic, Risk Factors, Respiratory infection, Diagnosis, Epidemiology, 030212 general & internal medicine, Hospital Mortality, Aged, 80 and over, Prediction theory, Age Factors, clinical epidemiology, Middle Aged, Tool, Emergency medicine, Female, Glomerular Filtration Rate, Pulmonary and Respiratory Medicine, Adult, Prognostic variable, medicine.medical_specialty, Medicina, Renal function, Diagnosis tripod, 03 medical and health sciences, Sex Factors, emergency medicine, Internal medicine, medicine, pneumonia, Humans, Derivation, Lymphocyte Count, Aged, Inpatients, Receiver operating characteristic, business.industry, SARS-CoV-2, Clinical epidemiology, COVID-19, Pneumonia, medicine.disease, Individual prognosis, critical care, Oxygen, Critical care, Logistic Models, Dyspnea, ROC Curve, Teoria de la predicció, Viral infection, viral infection, business, Kidney disease
Abstract

COVID-19@Spain and COVID@HULP Study., [Objective] To develop and validate a prediction model of mortality in patients with COVID-19 attending hospital emergency rooms., [Design] Multivariable prognostic prediction model., [Setting] 127 Spanish hospitals., [Participants] Derivation (DC) and external validation (VC) cohorts were obtained from multicentre and single-centre databases, including 4035 and 2126 patients with confirmed COVID-19, respectively., [Interventions] Prognostic variables were identified using multivariable logistic regression., [Main outcome measures] 30-day mortality., [Results] Patients’ characteristics in the DC and VC were median age 70 and 61 years, male sex 61.0% and 47.9%, median time from onset of symptoms to admission 5 and 8 days, and 30-day mortality 26.6% and 15.5%, respectively. Age, low age-adjusted saturation of oxygen, neutrophil-to-lymphocyte ratio, estimated glomerular filtration rate by the Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equation, dyspnoea and sex were the strongest predictors of mortality. Calibration and discrimination were satisfactory with an area under the receiver operating characteristic curve with a 95% CI for prediction of 30-day mortality of 0.822 (0.806–0.837) in the DC and 0.845 (0.819–0.870) in the VC. A simplified score system ranging from 0 to 30 to predict 30-day mortality was also developed. The risk was considered to be low with 0–2 points (0%–2.1%), moderate with 3–5 (4.7%–6.3%), high with 6–8 (10.6%–19.5%) and very high with 9–30 (27.7%–100%)., [Conclusions] A simple prediction score, based on readily available clinical and laboratory data, provides a useful tool to predict 30-day mortality probability with a high degree of accuracy among hospitalised patients with COVID-19., This work was supported by Fundación SEIMC/GeSIDA. The funders had no role in study design, data collection, data interpretation or writing of the manuscript. JB, JRB, IJ, JC, JP and JRA received funding for research from Plan Nacional de I+D+i 2013‐2016 and Instituto de Salud Carlos III, Subdirección General de Redes y Centros de Investigación Cooperativa, Ministerio de Ciencia, Innovación y Universidades, cofinanced by the European Development Regional Fund “A way to achieve Europe”, Operative program Intelligent Growth 2014‐2020. Spanish AIDS Research Network (RIS) (RD16/0025/0017 (JB), RD16/0025/0018 (JRA), RD16CIII/0002/0006 (IJ)). Spanish Network for Research in Infectious Diseases (REIPI) (RD16/0016/0001 (JRB), RD16/0016/0005 (JC) and RD16/0016/0009 (JP)).

Published
2021

14. Identification and validation of clinical phenotypes with prognostic implications in patients admitted to hospital with COVID-19: a multicentre cohort study

Author

Jaime Fernández-Bujarrabal Villoslada, Beatriz Dietl Gómez-Luengo, Daniel Ortiz-Sánchez, José Ramón Blanco Ramos, Bartolomé Gómez-Arroyo, Martín Sebastián Ruiz Grinspan, Ester Sáez de Adana Arróniz, Daniel Daniel López, Judit Villar-García, Begoña De Dios García, Josefina García García, Nuria Rabella García, Ana Rodríguez-Revillas, Lydia Martín González, Mercedes San Franco, Elena Martinez Robles, Teresa González Alegre, Elena Morcillo Rodríguez, Oriol Gasch Blasi, Laura Prieto Pérez, Isabel Jiménez Martínez, Elena Isaba Ares, Ricardo Deza-Palacios, Helena Mendez del Sol, Melchor Riera Jaume, Mercedes Rodriguez-Gutiérrez, Daniel Podzamczer, Mikel Urroz, Luis Ramos Ruperto, María Paniagua, Sergio Alcolea-Batres, Mar Masiá Canuto, Rubén Soriano-Arroyo, Paloma Merino Amador, Berta Antón-Huguet, Gabriela Alcaraz, Pablo Ryan, Carlos Franco, Leyre Díez-Porres, Juan Carlos Figueiras, Sara Lidia Kamal, Mónica Hernández, Lorena Barrera-López, Germán Ramírez-Olivencia, Kapil Laxman Nanwani Nanwani, Alberto Oreja, Montserrat Laguno, José Javier Castrodeza Sanz, Belén Loeches Yagüe, Maria Vargas, Luis Eduardo López-Cortés, Isabel Gutiérrez, Sara Vela Berna, P. Martín, Miguel Pedromingo Kus, Jesús Sanz Sanz, Mº Antonia Sepúlveda Berrocal, Carmen Yera Bergua, Juan Cuadros González, Julen Cadiñanos Loidi, Josefa Serralta Buades, María Concepción Prados Sánchez, Francesca Gioia, Iris Pedrola Gorrea, Francisco Arnaiz de las Revillas, Xabier Kortajarena Urkola, Laia Lorenzo-Esteller, Ruth Bravo-Lizcano, Angel Iniesta, Sofía González-García, Belén Martínez López, Agustín Rojas-Vieyra, Concepción García García, Raquel Cavallé-Pulla, Lucía Gómez García, Alicia Herrero, Carlos Jesús Dueñas Gutiérrez, Loreto Vidaur Tello, Carmen Fernández-Capitán, Victoria Lo-Iacono García, Cecilia Gómez-Domínguez, Adalgisa Falcone, María José Ruiz Rodríguez, Arancha Castellano, Miquel Hortos Alsina, María Concepción Nuñez, María Luisa Fernández Vidal, Jésica Abadia Otero, Natalia Moya-González, Albert Sabater Gil, Pedro de la Oliva, Ylenia María Conde-Alonso, Laura Castelo Corral, José Mº García de Lomas Guerrero, Verónica Pérez-Blanco, Isabel San Juan, Martina Archinà, Júlia Sellarés, Juan Carlos Ramos, Cintia María Martínez Mateu, Belén Fernández-Puntero, Andrea Torrecillas-Mainez, Luis Falgueras López, Carlos Carpio-Segura, María Gandullo-Moro, Francisco Abellán Martínez, Cristina Díez, Pilar Martín Dávila, Silvia Gómez-Zorrilla, María Pilar García García, Renzo Tejada-Sorados, María Dolores del Toro, E. Álvarez-Rojas, Gema Muñiz, Lucía Cajuela, María Novella Mena, Estel Pons Viñas, Andrea Pérez Rodríguez, Benito Almirante, Mónica Gozalo, Patricia Girón De Velasco-Sada, Camilo Sanz Zamudio, Ángeles García Flores, Joaquín López-Contreras González, Blanca Fabre-Estremera, Pelayo Fernández Cidón, María Martínez-Redondo, Paula Alejandra Hernández-Liebo, Juan Herrero, Marta Duque-Alcorta, María Teresa García Morales, Concepción Amador Prous, Alex Soriano, Raquel Hernando Nieto, Raquel Álvarez Franco, Alfonso Cabello Úbeda, Luis Force Sanmartín, Laura Mao Martín, Daniel Prieto-Arribas, Mario Pérez-Butragueño, Pere Domingo Pedrol, Henar Serrano-Martín, Mónica Zubimendi, M. Rodríguez-Rubio, David Pujol-Pocull, Manuel García-Gutiérrez, Carlos Manrique de Lara, Lucy Abella Vázquez, Marta Navarro Vilasaró, Carlota Cascajares-Sanz, Berta Torres, Daniel Ceniza-Pena, Isidro Moreno Gómez-Limón, María Rodríguez Mahía, Alí Martakoush, Antonio Buño-Soto, Patricia Serrano de la Fuente, Claudia González Rico, Teresa Pedraz, Conchita Pérez-Jorge Peremarch, Elena Trigo Esteban, Rosana Rouco Esteves Marques, Juan Mora Delgado, Inés Pérez Zapata, Sandra Pérez-Recio, María Ángeles Domínguez, Manuel Cervantes García, Francisco Reinoso-Lozano, M. Martí De Gracia, Carmina Oltra, Beatriz Pérez-Monte Mínguez, Guillermina Bejarano-Redondo, Sara Heili Frades, María Paz García Butenegro, Miguel Torralba González de Suso, Elena Álvaro-Alonso, Víctor J Moreno Cuerda, Gonzalo Garzón, Marcelo Daltro-Lage, Alberto Serrano Martínez, José María Aguado, Mar Mosquera, Ruth Figueroa Cerón, Juan Carlos Martin Gutiérrez, Javier Oliver Ortega, Esteban Martínez, Cristina Gómez-Ayerbe, Nerea Carrasco Antón, María Carmen Fariñas Álvarez, José Antonio Ruiz, Justo Menéndez, Lucía Díaz, José L. Casado, Pilar Vizcarra, Javier Veganzones, Miguel Ángel Moran Rodríguez, Mercedes López-Martinez, Emilio Letang, Paloma Romero Gallego-Acho, Julia Vasquez-Manau, Alexander Rombauts, Marta Robledo del Prado, Luis Puente, Beatriz Alvarez, Juan Emilio Losa García, José Tomas Algado Rabasa, Rafael Torres Perea, Angélica Rivera-Núñez, Esther Expósito Palomo, Antonio J. Carcas, Lucía Platero-Dueñas, Irene Martín Rubio, Miguel Salavert Lletí, Claudia García-Vaz, Antonio Martínez-Verdasco, Jorge Díaz-Garzón, Javier Nieto Arana, Fernando Cadenas-Gota, Richard Rojas, Abelardo García de Lorenzo, Juan Carlos López, Pedro Luis Martinez Hernández, Manuela de Pablos-Gómez, Pablo Alonso, Enrique Seco, María García-López, Lorena López-Corcuer, Celia Blasco-Andres, Delia Romera-Cano, José M. Azcona Gutiérrez, Almudena Gutiérrez-Arroyo, Paula Mendoza Roy, Ignacio De los Santos Gil, Miguel Angel Sánchez-Castellano, Sara Medrano Pardo, Mikel del Álamo Martínez de Lagos, Rocío Martínez Avilés, Elisabet Martínez-Cerón, José Manuel Vázquez Comendador, Marta Virgós-Varela, Alejandra Álvarez Brandt, Carmen Herrero Rodríguez, Jorge Martínez Jordán, Antonio Rezusta López, Marta Vizcaíno Callejón, Manuela Simon-Velasco, Jorge Ignacio Alonso-Eiras, Elisa García Vázquez, Mercè Gurguí Ferrer, Mónica González Bardanca, Nataly Cancelliere-Fernández, José Luis Díaz de Tuesta del Arco, María Larrosa, Alejandro García García, Carmen Román-Hernández, Elena Calvin-García, José Sanz Moreno, Miguel Silvestre-Niño, Nieves Valcarce Pardeiro, Maria Teresa Corcuera-Pindado, Enrique Monteoliva, Aina Gabarrell Pascuet, Elena María Aranda Rife, Aina Gomila Grange, Alba Alastrué Violeta, Daniel Roger Zapata, Jaime Montserrat, Eduardo Malmierca Corral, Marco Palma, Blanca Martínez Cifre, Gema Domínguez de Pablos, Emilio Cuesta, Eva Perales, Silvia Hernáez Crespo, Juan Torres-Macho, Adrián Sánchez Montalvá, Rocío Montejano Sánchez, Eva Van den Eynde Otero, Silvia Castañeda Espinosa, Virginia Pérez Doñate, Adriana Hernández Belmonte, Laura Iglesias Llorente, María Sanz de Pedro, Juan Espinosa Pereiro, Lubna Dani Ben-Abdellah, Raquel Barrós González, Iván Piñero, Araceli López-Tofiño, Ana Such-Diaz, Karim Mohamed Ramírez, Pilar Toledano Sierra, Rebeca Izquierdo, Guillermo Cuevas, Andrés Felipe Cardona Arias, Ileana Gabriela-Tomoiu, David Vinuesa García, Ander González Sarria, Stephan Stuart, José María Fernández, Javier Torres-Cortés, Elisabet Delgado Sánchez, María Varela-Cerdeira, Gemma Bassani, Berta Román Bernal, Isabel García, Paula Betancort de la Torre, Yolanda Martínez-Abad, Beatriz Arizcun, Juan José Cabanillas-Martín, Guillermo Estrada Fernández, Oscar del Río Pérez, Inmaculada Martín Pérez, Andony García, Luis Gómez-Carrera, Alexander Agrifoglio, Alberto M. Borobia, Jordi Niubó, Vanessa Alende Castro, Lara Montes Andújar, Alexandra De la Vega, Efrén Sánchez Vidal, Isabel A. Pérez Hernández, Laura Frade-Pardo, Ana Josefa Tebar-Martinez, Silvia Álvarez Kaelis, Sara De la Fuente Moral, Luz Martin Carbonero, Juan Cantón De Seoane, María Dolores Montero-Vega, Juan Carlos Gainzarain Arana, Sergio España Cueto, Rocío Nuñez-Cabetas, María Sánchez-Martín, Constanza Muñoz Hornero, Ana Gómez-Zamora, Javier Díaz Luperena, Patricia González-Donapetry, José Miguel Cisneros, Lucía Hernández-Rivas, Patricia González Ruano, Andrea Espigares Correa, Rocío González-León, Nicolás García-Arenzana, Omar Cervera, Andrés Canut Blasco, Ana Isabel Cañabate, Mercedes Villarreal García-Lomas, Melania Íñigo Pestaña, Maria Álvarez de Castro, Ana Correa Ruiz, Belén Civantos, Lydia Pascual-García, Paula Villares Fernández, Mikel Rico-Briñas, María José Alcaide-Martín, Adoración Valiente, Victoria Arnalich-Montiel, Pilar Retamar, Jesús Mingorance, Eva María Romay Lema, Pablo Galindo-Ballesteros, M. Teresa Pérez-Rodríguez, Rosario Maria Torres Santos-Olmo, Inmaculada Pinilla, Elie Dahdouh, Beatriz Tejero-Soriano, Cristina Pizarro-Sanchez, Félix Gutiérrez Rodero, Luis Jara-Palomares, María Hernández-Gancedo, Cristina Chico Chumillas, Sergio Gilaberte Reyzábal, Manuel González-Viñolis, Ana Martínez Sapiña, Francisco Parras, Teresa Rubio Obanos, Iker Falces-Romero, Adriana Sánchez Serrano, Teresa Álvarez de Espejo Montiel, Jorge Valencia, Miquel Pujol, José Luis Velasco Garrido, Belén Calderón-Llopis, Álvaro Varela Plaza, Abel Caro, Juan José González-Garcia, Miguel Sampedro Núñez, María Fernández-Velilla, Emilio Cendejas-Bueno, María Cecilia Cánepa, José Luis Santiago Blanco, Alicia Rico-Nieto, Mónica Liébana Gómez, Sarah Caro Bragado, Susana Sánchez-Rico, José María Marimón Ortiz de Zárate, Paloma Dorao, Cristina Plaza-Moreno, Isabel Valbuena, Natividad Benito Hernández, Ginger Giorgiana Cabrera Tejada, Jordi Carratalà, Sara Fernández Rodríguez, Vicente Ferrer Díaz De Brito Fernández, Pilar Catalán, Pablo Mariscal-Aguilar, Germán Daroca-Bengoa, Rafael Fernandez, Raquel Casitas-Mateo, Ester Zamarrón de Lucas, Úrsula Quesada, Julio Yagüe, María Isabel Quijano Contreras, Trinidad Baselga-Puente, Lourdes Herrera Pacheco, Carlota Gudiol, Alazne Lartategi Iraurgi, Estefanía Martinez-Chavez, Silvia Valero Rovira, Alba Bergas, Zaida Ruiz de Azua, Teresa Prim, Cristina García-Quero, Pilar Hernández Machín, Rubén Gomez-Rioja, María Pavón-Masa, María de las Mercedes Valentín-Pastrana Aguilar, Ilduara Pintos Pascual, Lucía Brieba-Plata, María Jesús Domínguez Santalla, Francisco Javier Membrillo de Novales, Raúl Galera-Martínez, Ana Lérida Urteaga, Miguel Cervero, Alberto Mangas-Moro, José Hernández Quero, Teresa Sancho Bueso, María Angustias Quesada Simón, Luz Parra-Gordo, Sofía Díaz-Carrasco, Juan Carlos Abad Almendro, Andrés Javier Ruiz Fernández, Estíbaliz Molina Iturritza, Aurea Díez-Tascón, Yale Tung-Chen, Marta Rava, Carlos Villasante, Gabriel Gaspar Alonso-Vega, Clara Cabré-Verdiell Surribas, Esther Fraile Villarejo, Aida Gutiérrez García, Ana Robustillo-Rodela, Rafael Padrós Selma, Jesús Rodríguez-Baño, Frank Perdomo-García, Lydia de la Fuente Regaño, María del Mar Arenas-Miras, Cristina Rodríguez Roca, Blanca Montero-San Martín, Gema Crespo-Sánchez, Miguel Ramírez-Verdyguer, Alberto Diaz de Santiago, Marta Díaz Menéndez, María de la Luz Padilla Salazar, Silvia Arribas-Terradillos, Sadaf Zafar Iqubal-Mirza, Isabel Rábago Lorite, Belén Estébanez, Maite Ganchegui Aguirre, André Barbosa Ventura, Estefanía Fernandez-Cerezo, Maria Eulalia Valencia, Zaira R. Palacios-Baena, Beatriz Diaz Pollan, Lidia Martín, Sara Fabra-Cadenas, José Miguel Cantero-Escribano, Carmen Busca Arenzana, Emilia Guasch-Arévalo, Virginia Fernández Espinilla, Ainhoa Urrutia Losada, Oscar Noya González, Raquel Aranega, Alejandro Rodríguez Saenz de Urturi, María Jesús Jaras Hernandez, Charbel Maroun Eid, Marta Mora Rillo, Antonio Ramos Martínez, Meritxell Ortega Montoliu, Jose María Mostaza, Sonia García Calvo, Cristina Verdú, Celia Salamanca, Cristina Cervera Acedo, Mónica Martínez, Miren Urrestarazu Larrañag, Carmen Barroso Castro, Ivo Vives-Beltrán, Lorea Arteche Eguizabal, Ana Montero, Javier Balsa Vázquez, Amparo Perez-Garcia Morillón, Alejandra Pérez García, Isabel Pérez-Tamayo, Rafael Cantón Moreno, Antonio Marín-García, Inmaculada Jarrín, Núria Trullen, Ines Fernandez-Jimenez, Guillermo Ruiz-Carrascosa, Almudena Villa Martí, Jamil Cedeño, Marcos Díez Martínez, Carlos Lahoz, Lorena De la Mora, Javier Sánchez-Lora, Ana María Martínez-Virto, Irene Sanjosé Muñiz, Adrian Peña-Hidalgo, Cristina López Mestanza, Carola Gutiérrez, Ana Laila Qasem-Moreno, Irene Salvo García, Lucía Fernández de Orueta, Jorge Parra Ruiz, Sergio Pérez Pinto, Carlos García-Mochales Fortún, Esteban García de las Heras, Patricia González Muñiz, Mario Fernández-Ruiz, Anna Ferrer Santolaria, Olga Sánchez Pernaute, Julieta Latorre, Jesús Manzanares, Miguel Angel Martinez Gallego, Helena Notario, Ángel Rodríguez-Villodres, Eva Fernández-Bretón, Encarnación Moral Escudero, Mónica Sánchez-Santiuste, Carmen Martínez Cilleros, Ricardo Fernández Roblas, María Yllescas, Eva Soria-Alcaide, Marta Arsuaga Vicente, Marta Gómez-López, Regina Cabrera-Gamero, Natalia Carrasco Fons, Diana Piñar Cabezos, Begoña Sánchez-Sánchez, Francisca Garcia-Iglesias, Raquel Marín-Baselga, Alberto Arranz Caso, Virginia Guedez-López, Lucia Boix Palop, Íñigo Gredilla Zubiría, María Hidalgo-Sánchez, Laura López-Tappero Irazábal, José Ignacio Bernardino de la Serna, Javier Queiruga, Natalia Guadalupe Barrera-López, María López-Jodar, Jorge Calderón Parra, Diego Rodríguez-Álvarez, José Molina, María Luisa Montes, Beatriz Rodríguez-Alonso, Daniel Useros Brañas, Maria Gracia Liras-Hernández, Lucía Romero-Imaz, Nieves Jaén Sánchez, Marta Segovia-Amaro, Marta Vara, Maribel Zamora Cintas, Montaña Jiménez Álvaro, Alberto Moreno Fernandez, Asunción Díaz, Jordi Mancebo Cortés, Francisco Javier De Castro Vega, Álvaro Navarro Batet, Francisco Javier Sagra, Alexandre Pérez González, Luis Castro, Isabel Barrio López, Marta Ruiz-Alguero, Silvia Ossaba-Vélez, Alberto Martín-Vega, Maria Jesus Bustinduy Odriozola, Sivia Pastor-Yvorra, Nuria Espinosa, Elena Múñez Rubio, María E García-Leoni, Sandra Rosillo, Cristina Carbonell, Iván Navas Clemente, Paula Arriola Martínez, Marta Peña, Lucía Martínez de Soto, Roberto Mora-Corcovado, Alberto Iglesias-Sigüenza, Rocío Ruíz-Hueso, Elena Alvar, Pedro Camacho, Jesús Sojo-Dorado, Remedios Alemán Valls, Ines Ponz, Esmeralda Palmier Peláez, María Arcos Rueda, Guillermo Maestro de la Calle, Ramón Pérez Tanoira, Ana Martínez Vidal, Cristina Amodeo, Marina Pacheco Martínez-Atienza, Clara Muñoz Aguirre, Felipe Villar Álvarez, Giorgina Salgueiro, Xavier Sanz Salvador, César Pérez-Romero, Beatriz Álvarez Zapatero, Nelsa González-Aguado, Robert Torres Sánchez del Arco, Enrique Míguez Rey, Merce Sirisi, Xavier Bonfill Cosp, Marta Yagüe-Barrado, Elena Pérez-Costa, Sandra Casares, Eva Estirado, Jorge Alvarez Troncoso, Cristina Martín-Carrasco, Diana Sande Llovo, Melchor Álvarez de Mon Soto, Arantzazu Mera Fidalgo, Francisco Marqués-González, Agustín Valido-Morales, Luis Alberto Nieto Fernández del Campo, Helem Haydee Vilchez, María Rivas-Carmenado, Francisco Moreno, Ignacio Fernández-Fernández, Henar Calvo Sánchez, Ana González-Cordón, Isabel Fernández-Navarro, María Simón Sacristán, Eva Jiménez-González de Buitrago, M. Muñoz, María Laplaza-González, Rosa de Miguel Buckley, Marta Redondo-Gutierrez, Paula Santibáñez Sáenz, Raquel Martínez Goñi, Marta Rico Rodríguez, Carlos Toro-Rueda, Francisco Arnalich, Ana Santiago-Recuerda, Clara Soto Abanedes, María Dolores Herrero Mendoza, Aquilino Sanchez Purificación, Diego Franch Llasat, María Velasco Arribas, Alejandro Martín-Quirós, Jorge Alba Fernández, Elena Ramírez, Amparo López-Bernus, Marta Alvarado, María Rexach Fumaña, Martín Pilares-Barco, Carmen Liébana Martos, Yolanda Martínez Martínez, Nicolas Merchante Gutiérrez, Maria José Asensio, Ianire Virto Peña, Lucía Mejuto-Illade, María Angeles Martinez-López, Pilar López-Pirez, Alejandro Suárez, Cristóbal Manuel Rodríguez Leal, Sara Garcia-Bellido Ruiz, Jorge Guisández Martín, Lucia Cachafeiro, Pedro Gil Divasson, Almudena Quintás-Viqueira, Laura Currás-Sánchez, Alverio Seiz-Martinez, Mario Ruiz-Bastián, Juan José Menéndez, Jorge Orihuela Martín, María Dolores Nieto Martín, Cristina Arévalo, Rebeca Marinas, Susana Casas Rodríguez, Zuriñe Ortiz de Zárate Ibarra, Yolanda Posada Franco, Joan Gómez-Junyent, Ana María Garijo Saiz, Marina Alguacil-Guillén, Ana Alguacil, Esther Aznar Muñoz, Sara Bañón Escandell, Juan Salillas Hernando, Chiara Fanciulli, Rosa Gómez-Gil, Francisco García-Río, Moncef Belhassen-García, Belén Gutierrez Sancerni, Sonia Vega Molpeceres, Inés Suárez-García, Leire Pérez-Latorre, Elena Chamarro Martí, Carmen Rosario Herrero Gil, Belén Gutiérrez-Gutiérrez, Tatiana Mata Forte, Francesca Sánchez Martínez, Lucía Ramos Merino, Santiago Yus, Mº Ángeles Marcos, Susana Martínez-Álvarez, Alexy Inciarte, Manuel Quintana-Díaz, Lucía Serrá, Belén Alejos, Guillem Policarpo Torres, José Román Muñoz del Rey, Irene Blanco-Bartolomé, Alberto Bahamonde Carrasco, Victoria Hernando, Jhon Rojas, David Roa, María Ángeles Garcinuño, Aránzazu Villasante de la Puente, Patricia Pérez-Palacios, Jesús Ruiz Aragón, Valvanera Ibarra Cucalón, Lucía Ortega Enciso, Ismail Zakariya-Yousef Breval, Jorge Navarro López, Gema Barbeito Castiñeiras, Clara Sala Jofre, Nora Molina Torres, Manuel Poyato, Inmaculada Poquet Catala, Virginia Pomar Solchaga, María Pilar Romero-Gómez, Clara Hernández, Helena Mozas Moriñigo, Mercedes Guillamón Sánchez, Zineb Karroud, Arianna Catino, Violeta Ramos Sesma, Santos del Campo, Pilar Fernández-Calle, Ana Fernández Cruz, Fernando Salvador, Rosa Mayayo-Alvira, Pilar Barco Núñez, Ana Isabel Peláez Ballesta, Silvia Suárez Diaz, Beatriz María Sanjuan, Nora Izko Gartzia, Teresa Aldámiz-Echevarría, Cecilia Tortajada Alamilla, Pau Bosch-Nicolau, María del Mar Alonso Socas, Sonia Calzado Isbert, Jose R. Arribas, Juan Fernández-Lahera, Elizabet Petkova Saiz, Eva Jiménez, Gabriela Abelenda-Alonso, Alba Ribera Puig, Pascual Sanabria-Carretero, Sara Rodrigo González, Irene Díaz de la Torre, Tamara Manso Gómez, Carmen Sáez Barberá, Roi Suárez Gil, Paloma García-Clemente, Héctor Meijide Míguez, Elsa Izquierdo-García, Josune Goikoetxea Agirre, Olalla Martínez Macia, Jesús Santos González, Guillermo Jiménez Álvarez, Cristina Marcelo-Calvo, Javier Coy Coy, Isabel Arenas-Berenguer, Julio García Rodríguez, Natalia Yustas-Benitez, Sarai Quirós-Fernández, Marina Noguerol-Gutiérrez, María Adalid Moll, Iván Bloise-Sánchez, Mario José Rodriguez Dominguez, Elena Salamanca, Francisco Mora Gómez, Lucio García-Fraile, Pablo Millán, C Gutiérrez, Montserrat Rodríguez, José Antonio Oteo Revuelta, Joseba Portu Zapirain, Cristina Moreno, Irene Carrillo Acosta, Jorge Calvo, Ana Mariño Callejo, David Romero-Ribate, Blanca Alonso, Elena Muñoz del Val, Elena Resino Foz, Olaia Rodriguez-Fraga, Miguel Villamarín, Irene Amores-Hernández, Laura Muñoz López, Esther García Almodóvar, Ismael Casares Guerrero, Angélica Villanueva-Freije, Nuria Parra Arribas, Montserrat Sanmarti Vilamala, Macarena Lerín-Baratas, Mercedes Castro-Martínez, Melissa Carreres Candela, Lucia Suárez Pérez, Jose Manuel Iturzaeta-Sánchez, Thamires Silva-Freire, José Antonio Peregrina, María Luisa Machado Sicilia, Sergio Zurita, Daniel Molina Morant, Olga González-Peña, Fernando Lázaro-Perona, Paloma Oliver-Saez, Beatriz Mestre-Gómez, Luis Díaz Díez Picazo, Silvia García-Bujalance, Francisco Rodríguez Gómez, Pere Comas Casanova, Carlos Ruiz Martínez, Alberto Delgado-Iribarren, Berta Alonso-González, Isabel Moreno-Parra, Teresa Gómez-Ballesteros, Araceli Menéndez, Jose Manuel Añón, Ruth Jorge García, Jonathan Cámara Fernández, Miguel Górgolas Hernández-Mora, Itziar Diego Yagüe, Miriam Latorre-Millán, Covadonga Morcate Fernández, M. Río-García, Elisabet Lerma-Chippirraz, Carmen Yllera Gutiérrez, Francesc Albertí, Eva Flores, Carmen R. Uña Orejón, Patricio González-Pizarro, Neila Rodriguez-Roca, Miguel Fernández-Huerta, Inés Ferrer Ortiz, María José Blanco Vidal, Juan Pablo Avilés, Alicia Lorenzo Hernández, Mireia Puig Campmany, José Bravo-Ferrer, Gonzalo Martínez-Alés, Pablo Marguenda Contreras, M. Sánchez, Antonio García Pardo, Yolanda Meije, Francisco Tejerina, Carolina Hernández Carballo, Victoria Moreno, Daniel Laorden-Escudero, Ana Barrios Blandino, Alexia Costanza Espiño Álvarez, Ana Milagro Beamonte, Jerónimo Pachón, S San José-Villar, Marta Morando, María del Carmen Navarro Sáez, Rodolfo Álvarez-Sala Walther, Jon Ugalde Espiñeira, Fernando De la Calle Prieto, Nuria Fernández, Iván Pelegrín Senent, Alba Rueda López, Cristina Schüffelmann, Marcelino Hayek Peraza, Laura Labajo-Montero, Angel Robles Marhuenda, Pilar Durán, Ana Esteban-Romero, María Rosa Oltra Sempere, Ana Cosmen Sánchez, Alex Smithson Amat, Margarita Ramírez-Schacke, Marco Antonio Sempere Alcocer, Paloma Carrera-Vázquez, M Miarons, Teresa García Delange, Amelia Rodriguez-Mariblanca, Eva Talavera García, Roberto Vates Gómez, Óscar Sanz Peláez, José María Muñoz-Ramón, José Luis García Fogeda, Isabel Arroyo-Rico, Verónica Cano Llorente, Fernando González-Romo, Alberto Alonso-Babarro, Fátima Brañas, Fabricio Iannuccelli, Pilar Álvarez Padín, Luis Metola Sacristán, Vicente Boix, Víctor Hontañón, Juan Berenguer, José Luís Del Pozo León, Patricia Sorní Moreno, Maria Isabel Torres, Rafael Mican Rivera, Amparo Blasco Claramunt, Carmen Ardanuy, Aychel Elena Roura Piloto, María Ángeles Molina, Isabel Asschert Agüero, Julía Alvárez del Vayo, Consuelo García-Sánchez, Begoña Reche-Martínez, Guillermo Cuervo, Carlos Iniesta, María Antonia Gómez-Mendieta, Ana María Noblejas Mozo, Andres Bartrina-Tarrio, Carmen De la Higuera Arranz, Yeray Untoria Tabares, Andrés Enrique Suárez-Plaza, Jesús Frías, Paloma López-Arévalo, Irene María Llorente-Cortijo, Instituto de Salud Carlos III, Ministerio de Ciencia e Innovación (España), and Fundación SEIMC-GESIDA

Subjects
Male, Prognostic variable, medicine.medical_specialty, Databases, Factual, Coronavirus disease 2019 (COVID-19), 030204 cardiovascular system & hematology, Cohort Studies, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, Humans, Medicine, 030212 general & internal medicine, Aged, Retrospective Studies, Models, Statistical, SARS-CoV-2, business.industry, Mortality rate, COVID-19, Retrospective cohort study, Articles, Middle Aged, Prognosis, medicine.disease, Phenotype, Hospitals, Hospitalization, Logistic Models, Infectious Diseases, Spain, Cohort, Female, Lymphocytopenia, business, Cohort study
Abstract

REIPI-SEIMC COVID-19 group and COVID@HULP group., [Background] The clinical presentation of COVID-19 in patients admitted to hospital is heterogeneous. We aimed to determine whether clinical phenotypes of patients with COVID-19 can be derived from clinical data, to assess the reproducibility of these phenotypes and correlation with prognosis, and to derive and validate a simplified probabilistic model for phenotype assignment. Phenotype identification was not primarily intended as a predictive tool for mortality., [Methods] In this study, we used data from two cohorts: the COVID-19@Spain cohort, a retrospective cohort including 4035 consecutive adult patients admitted to 127 hospitals in Spain with COVID-19 between Feb 2 and March 17, 2020, and the COVID-19@HULP cohort, including 2226 consecutive adult patients admitted to a teaching hospital in Madrid between Feb 25 and April 19, 2020. The COVID-19@Spain cohort was divided into a derivation cohort, comprising 2667 randomly selected patients, and an internal validation cohort, comprising the remaining 1368 patients. The COVID-19@HULP cohort was used as an external validation cohort. A probabilistic model for phenotype assignment was derived in the derivation cohort using multinomial logistic regression and validated in the internal validation cohort. The model was also applied to the external validation cohort. 30-day mortality and other prognostic variables were assessed in the derived phenotypes and in the phenotypes assigned by the probabilistic model., [Findings] Three distinct phenotypes were derived in the derivation cohort (n=2667)—phenotype A (516 [19%] patients), phenotype B (1955 [73%]) and phenotype C (196 [7%])—and reproduced in the internal validation cohort (n=1368)—phenotype A (233 [17%] patients), phenotype B (1019 [74%]), and phenotype C (116 [8%]). Patients with phenotype A were younger, were less frequently male, had mild viral symptoms, and had normal inflammatory parameters. Patients with phenotype B included more patients with obesity, lymphocytopenia, and moderately elevated inflammatory parameters. Patients with phenotype C included older patients with more comorbidities and even higher inflammatory parameters than phenotype B. We developed a simplified probabilistic model (validated in the internal validation cohort) for phenotype assignment, including 16 variables. In the derivation cohort, 30-day mortality rates were 2·5% (95% CI 1·4–4·3) for patients with phenotype A, 30·5% (28·5–32·6) for patients with phenotype B, and 60·7% (53·7–67·2) for patients with phenotype C (log-rank test p, [Interpretation] Patients admitted to hospital with COVID-19 can be classified into three phenotypes that correlate with mortality. We developed and validated a simplified tool for the probabilistic assignment of patients into phenotypes. These results might help to better classify patients for clinical management, but the pathophysiological mechanisms of the phenotypes must be investigated., [Funding] Instituto de Salud Carlos III, Spanish Ministry of Science and Innovation, and Fundación SEIMC/GeSIDA., Funding: Instituto de Salud Carlos III, Spanish Ministry of Science and Innovation, and Fundación SEIMC/GeSIDA.

Published
2021

15. Genomic Analysis of Early SARS-CoV-2 Variants Introduced in Mexico

Author

Santiago Ávila-Ríos, Ricardo Grande, Jorge Salas-Hernández, Adnan Araiza-Rodríguez, Celia Boukadida, Gloria Vazquez, Susana López, José Esteban Muñoz-Medina, Irma López-Martínez, Francisco Pulido, Lucía Hernández-Rivas, Marina Escalera-Zamudio, Rogelio Pérez-Padilla, Francisco Javier Gaytán-Cervantes, Pavel Isa, Edgar Mendieta-Condado, José Ernesto Ramírez-González, José Arturo Martínez-Orozco, Gisela Barrera-Badillo, César González-Bonilla, Pilar Ramos-Cervantes, Fabiola Garcés-Ayala, Joel A. Vazquez-Perez, Concepción Grajales-Muñiz, Carlos F. Arias, Alejandro Sanchez-Flores, Víctor Hugo Borja-Aburto, Eduardo Becerril-Vargas, Carolina Gonzalez-Torres, Blanca Taboada, and Guillermo M. Ruiz-Palacios

Subjects
Lineage (genetic), Pneumonia, Viral, Immunology, Genomics, Genome, Viral, Microbiology, chemistry.chemical_compound, Betacoronavirus, Phylogenetics, Molecular marker, Phylogenomics, Virology, Pandemic, Humans, Mexico, Pandemics, Phylogeny, biology, SARS-CoV-2, Outbreak, COVID-19, Computational Biology, Genetic Variation, biology.organism_classification, chemistry, Amino Acid Substitution, Genetic Diversity and Evolution, Evolutionary biology, Insect Science, Mutation, Coronavirus Infections
Abstract

The coronavirus disease 2019 (COVID-19) pandemic has affected most countries in the world. Studying the evolution and transmission patterns in different countries is crucial to enabling implementation of effective strategies for disease control and prevention. In this work, we present the full genome sequence for 17 SARS-CoV-2 isolates corresponding to the earliest sampled cases in Mexico. Global and local phylogenomics, coupled with mutational analysis, consistently revealed that these viral sequences are distributed within 2 known lineages, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage A/G, containing mostly sequences from North America, and lineage B/S, containing mainly sequences from Europe. Based on the exposure history of the cases and on the phylogenomic analysis, we characterized 14 independent introduction events. Additionally, three cases with no travel history were identified. We found evidence that two of these cases represented local transmission cases occurring in Mexico during mid-March 2020, denoting the earliest events described for the country. Within this local transmission cluster, we also identified an H49Y amino acid change in the Spike protein. This mutation represents a homoplasy occurring independently through time and space and may function as a molecular marker to follow any further spread of these viral variants throughout the country. Our results provide a general picture of the SARS-CoV-2 variants introduced at the beginning of the outbreak in Mexico, setting the foundation for future surveillance efforts. IMPORTANCE Understanding the introduction, spread, and establishment of SARS-CoV-2 within distinct human populations as well as the evolution of the pandemics is crucial to implement effective control strategies. In this work, we report that the initial virus strains introduced in Mexico came from Europe and the United States and that the virus was circulating locally in the country as early as mid-March. We also found evidence for early local transmission of strains with a H49Y mutation in the Spike protein, which could be further used as a molecular marker to follow viral spread within the country and the region.

Published
2020
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16. Genome Sequence of a Rabies Virus Isolated from a Dog in Chiapas, Mexico, 2013

Author

Belem Torres-Longoria, Israel Animas-Vargas, Martin Melo-Munguía, Elizabeth González-Durán, José Ernesto Ramírez-González, José Alberto Díaz-Quiñonez, Edgar Mendieta-Condado, Joanna Ortiz-Alcantara, Albert Sandoval-Borja, Sandra Perez-Agueros, Lucía Hernández-Rivas, Beatriz Escamilla-Ríos, Rita Terán-Toledo, Fabiola Garcés-Ayala, Irma López-Martínez, Nidia Aréchiga-Ceballos, Mauricio Gómez-Sierra, Susana Chávez-López, and David Martínez-Solís

Subjects
0301 basic medicine, Genus Lyssavirus, Whole genome sequencing, Lineage (genetic), Rabies virus, Biology, medicine.disease, medicine.disease_cause, Virology, 03 medical and health sciences, 030104 developmental biology, Viruses, Genetics, medicine, Molecular Biology, Encephalitis, Sequence (medicine)
Abstract

Rabies virus (RABV), a member of the genus Lyssavirus , causes encephalitis that is almost always fatal following the onset of clinical signs. Here, we report the complete codifying sequence of an RABV isolated from a dog in Mexico. Molecular data showed that this strain belongs to the Chiapas lineage.

Published
2018

17. Genotypic variability analysis of DENV-1 in Mexico reveals the presence of a novel Mexican lineage

Author

Mauricio Vázquez-Pichardo, José Ernesto Ramírez-González, Lucía Hernández-Rivas, Jesus Torres-Flores, Joanna Ortiz-Alcantara, Everardo Curiel-Quesada, Hugo G. Castelán-Sánchez, Alfonso Méndez-Tenorio, Belem Torres-Longoria, Irma López-Martínez, José Alberto Díaz-Quiñonez, Elizabeth González-Durán, Fabiola Garcés-Ayala, Jorge Membrillo-Hernández, and Juan Santiago Salas-Benito

Subjects
0301 basic medicine, Adult, Male, Adolescent, Genotype, viruses, Lineage (evolution), Biology, Evolution, Molecular, 03 medical and health sciences, Phylogenetics, Virology, Genetic variation, Humans, Severe Dengue, Child, Mexico, Phylogeny, Genetics, Molecular Epidemiology, Molecular epidemiology, Phylogenetic tree, virus diseases, Genetic Variation, General Medicine, biochemical phenomena, metabolism, and nutrition, Dengue Virus, Middle Aged, Founder Effect, Phylogeography, 030104 developmental biology, RNA, Viral, Female, Founder effect
Abstract

Here, we report for the first time the circulation of dengue virus type 1 (DENV-1) belonging to the lineage IV of genotype V (African American genotype) based on phylogenetic analysis of nucleotide sequences from 10 DENV-1-positive samples obtained in Mexico between 2012 and 2014. Our data revealed that the lineages III and IV of DENV-1 genotype V were found circulating during the same period, probably explaining the rise in the number of cases of severe dengue during that period.

Published
2017

18. Full genome and phylogenetic analysis of hepatitis B virus genotype F in Mexican isolates

Author

David Esaú Fragoso-Fonseca, Lucía Hernández-Rivas, José Ernesto Ramírez-González, Noé Escobar-Escamilla, Lourdes Teresa Lloret y Sánchez, Claudia Wong-Arámbula, and José Alberto Díaz-Quiñonez

Subjects
0301 basic medicine, medicine.medical_specialty, Hepatitis B virus, Hepatitis B virus genotype F, Genotype, Genome, Viral, Biology, Genome, 03 medical and health sciences, 0302 clinical medicine, Medical microbiology, Virology, medicine, Humans, Mexico, Phylogeny, DNA Primers, Whole genome sequencing, Hepatitis B Surface Antigens, Phylogenetic tree, virus diseases, General Medicine, Sequence Analysis, DNA, South America, Hepatitis B, digestive system diseases, 030104 developmental biology, DNA, Viral, 030211 gastroenterology & hepatology
Abstract

Hepatitis B virus genotype F (HBV/F) is endemic in Central and South America with a minor proportion in Mexico and North America. HBV/F is divided into subgenotypes and subtypes with particular geographic circulation patterns. Here, we report the complete genome sequence and molecular characterization of HBV/F from three isolates. Phylogenetic analysis with all available HBV/F sequences showed that our sequences belonged to the F1b subtype and, in addition, the absence of the previously reported F1a subtype in Mexican isolates. Our findings suggest the circulation of HBV/F1b, the first phylogenomic study of HBV/F in Mexico.

Published
2017

19. Molecular characterization of atypical antigenic variants of canine rabies virus reveals its reintroduction by wildlife vectors in southeastern Mexico

Author

Joanna Ortiz-Alcantara, Sandra Perez-Agueros, Lucía Hernández-Rivas, Belem Torres-Longoria, Elizabeth González-Durán, José Ernesto Ramírez-González, Irma López-Martínez, Nidia Aréchiga-Ceballos, José Alberto Díaz-Quiñonez, Fabiola Garcés-Ayala, and Alfonso Méndez-Tenorio

Subjects
0301 basic medicine, medicine.medical_specialty, Lineage (genetic), Genotype, Rabies, 030106 microbiology, Biology, Disease Vectors, medicine.disease_cause, Virus, 03 medical and health sciences, Medical microbiology, Dogs, Virology, medicine, Disease Transmission, Infectious, Animals, Cluster Analysis, Humans, Dog Diseases, Rabies transmission, Mexico, Phylogeny, Molecular Epidemiology, Molecular epidemiology, Rabies virus, General Medicine, Sequence Analysis, DNA, medicine.disease, 030104 developmental biology, RNA, Viral, Viral disease, Mephitidae
Abstract

Rabies is an infectious viral disease that is practically always fatal following the onset of clinical signs. In Mexico, the last case of human rabies transmitted by dogs was reported in 2006 and canine rabies has declined significantly due to vaccination campaigns implemented in the country. Here we report on the molecular characterization of six rabies virus strains found in Yucatan and Chiapas, remarkably, four of them showed an atypical reaction pattern when antigenic characterization with a reduced panel of eight monoclonal antibodies was performed. Phylogenetic analyses on the RNA sequences unveiled that the three atypical strains from Yucatan are associated with skunks. Analysis using the virus entire genome showed that they belong to a different lineage distinct from the variants described for this animal species in Mexico. The Chiapas atypical strain was grouped in a lineage that was considered extinct, while the others are clustered within classic dog variants.

Published
2017

20. Nontuberculous mycobacteria in clinical samples with negative acid-fast bacilli

Author

Isaura Isabel Martínez-Rivera, Heleodora González-González, José Ernesto Ramírez-González, Abril Paulina Rodríguez-Maldonado, Benita Pilar Torres-Mazadiego, Raúl Cicero-Sabido, Alejandro Hernández-Solís, Claudia Wong-Arámbula, América Del Pilar Mandujano-Martínez, Maribel González-Villa, and Lucía Hernández-Rivas

Subjects
Adult, DNA, Bacterial, Male, 0301 basic medicine, Microbiology (medical), Bacilli, Tuberculosis, Adolescent, nontuberculosis mycobacteria, 030106 microbiology, Antitubercular Agents, lcsh:QR1-502, Mycobacterium Infections, Nontuberculous, lcsh:Microbiology, Microbiology, Tertiary Care Centers, Young Adult, 03 medical and health sciences, PCR sequencing, 0302 clinical medicine, Humans, Medicine, Prospective Studies, Mexico, Phylogeny, Aged, Staining and Labeling, biology, business.industry, Nontuberculous Mycobacteria, Mycobacterium tuberculosis, Middle Aged, bacterial infections and mycoses, biology.organism_classification, medicine.disease, Active tuberculosis, Biological materials, Bacterial Typing Techniques, Infectious Diseases, 030228 respiratory system, Mycobacterium tuberculosis complex, Acid-fast, Female, Nontuberculous mycobacteria, business, Mycobacterium
Abstract

Background: There is a progressive increase in nontuberculous mycobacteria (NTM) in pulmonary and extrapulmonary infections that might cause confusion with the Mycobacterium tuberculosis complex. To determine the frequency of finding NTM in clinical samples from patients diagnosed with active tuberculosis, with negative acid-alcohol-resistant bacilli (acid-fast bacillus [AFB]) in a third-level specialty hospital's mycobacterial laboratory between January 2013 and December 2014. Methods: This is a prospective, descriptive study where isolated strains of biological material were studied in Lowenstein–Jensen and BACTEC MGIT 960 cultures. Results: Clinical samples of 120 patients were studied, with pulmonary samples of 99/120 (82%) and extrapulmonary samples of 21/120 (18%). We identified NTM in 37/120 samples (30.8%), of which 16 in pulmonary, 13 in genitourinary, 3 in bone marrow, and 5 in various specimens. Mycobacterium avium was isolated in 20 samples, Mycobacterium intracellulare in seven samples, and various other species of NTM in the other 10 samples. Conclusion: To establish adequate treatment, we point out the importance of identifying the presence of NTM in the clinical samples of active tuberculosis patients with negative AFB, as possibly becoming confused with M. tuberculosis and which is essential in deciding which treatment is the most adequate.

Published
2017

21. Nontuberculous mycobacteria in clinical samples with negative acid-fast bacilli

Author

Alejandro Hernandez-Solís, Raúl Cicero-Sabido, Maribel González-Villa, Isaura Isabel Martínez-Rivera, América del Pilar Mandujano-Martínez, Benita Pilar Torres-Mazadiego, Claudia Elena Wong-Arámbula, Abril Paulina Rodríguez-Maldonado, Lucia Hernández-Rivas, Heleodora González-González, and José Ernesto Ramírez-González

Subjects
Mycobacterium tuberculosis, nontuberculosis mycobacteria, PCR sequencing, Microbiology, QR1-502
Abstract

Background: There is a progressive increase in nontuberculous mycobacteria (NTM) in pulmonary and extrapulmonary infections that might cause confusion with the Mycobacterium tuberculosis complex. To determine the frequency of finding NTM in clinical samples from patients diagnosed with active tuberculosis, with negative acid-alcohol-resistant bacilli (acid-fast bacillus [AFB]) in a third-level specialty hospital's mycobacterial laboratory between January 2013 and December 2014. Methods: This is a prospective, descriptive study where isolated strains of biological material were studied in Lowenstein–Jensen and BACTEC MGIT 960 cultures. Results: Clinical samples of 120 patients were studied, with pulmonary samples of 99/120 (82%) and extrapulmonary samples of 21/120 (18%). We identified NTM in 37/120 samples (30.8%), of which 16 in pulmonary, 13 in genitourinary, 3 in bone marrow, and 5 in various specimens. Mycobacterium avium was isolated in 20 samples, Mycobacterium intracellulare in seven samples, and various other species of NTM in the other 10 samples. Conclusion: To establish adequate treatment, we point out the importance of identifying the presence of NTM in the clinical samples of active tuberculosis patients with negative AFB, as possibly becoming confused with M. tuberculosis and which is essential in deciding which treatment is the most adequate.

Published
2017
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