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

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 ß-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.

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

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.

Identificación de Mycobacterium bovis en pacientes con diagnóstico de tuberculosis pulmonar y extrapulmonar.

INTRODUCTION: In Mexico, there is an alarming increase in the number of cases of Mycobacterium bovis infection on pulmonary and extrapulmonary presentations. The lack of timely identification triggers complications and increases mortality. OBJECTIVE: To know the frequency of M. bovis infections in clinical samples of patients with tuberculosis in the mycobacteria laboratory of a reference hospital in Mexico City. METHOD: Prospective, descriptive study. Strains isolated from biological material were studied in Löwestein-Jensen and MGITI960 cultures. M. bovis was identified by amplifying the RD9 fragment with end-point polymerase chain reaction (PCR). RESULTS: Eight-hundred and fifty tuberculosis-diagnosed patients were included; in 441 cases, Mycobacterium tuberculosis was confirmed by positive culture (250 pulmonary, 65 ganglionic, 39 renal, 34 meningeal, 25 miliary, 14 pleural, 8 peritoneal, 4 bone and 2 pericardial cases). Forty-eight strains (10.8%) were typified as M. bovis by amplification of the RD9 fragment with end-point PCR. CONCLUSIONS: M. bovis is not currently thought of a causative agent of tuberculosis, which could be the cause of pharmacological treatment failure. In this study, the main extrapulmonary form was observed to be cervical lymphadenopathy.

INTRODUCCIÓN: En México existe un incremento alarmante de casos de infección pulmonar y extrapulmonar por Mycobacterium bovis. La falta de identificación oportuna deriva en complicaciones y eleva la mortalidad. OBJETIVO: Conocer la frecuencia de infecciones por Mycobacterium bovis en muestras clínicas de pacientes con tuberculosis, identificadas en el laboratorio de micobacterias en un hospital de concentración de la Ciudad de México. MÉTODO: Estudio prospectivo, descriptivo. Se estudiaron cepas aisladas de material biológico en cultivos Löwestein-Jensen y MGITI960. La identificación de Mycobacterium bovis se realizó mediante la amplificación del fragmento RD9 por PCR punto final. RESULTADOS: Se incluyeron 850 pacientes con diagnóstico de tuberculosis, en 441 casos se confirmó Mycobacterium tuberculosis por cultivo positivo (250 casos pulmonares, 65 ganglionares, 39 renales, 34 meníngeos, 25 miliares, 14 pleurales, ocho peritoneales, cuatro óseos y dos pericárdicos). Se tipificaron 48 cepas (10.8 %) como Mycobacterium bovis por amplificación del fragmento RD9 por PCR punto final. CONCLUSIONES: Actualmente no se piensa en Mycobacterium bovis como agente causal de tuberculosis, lo que pudiera ser la causa del fracaso del tratamiento farmacológico. En este estudio se observó que la principal forma extrapulmonar es la linfadenopatía cervical.

Nontuberculous mycobacteria in cervical lymphadenopathies of HIV positive and HIV-negative adults / Micobacterias no tuberculosas en linfadenopatías cervicales de adultos VIH positivos y VIH negativos

Background: Tuberculosis is a global public health problem, especially in emerging countries. Mycobacterium tuberculosis is the main cause of cervical lymphadenopathy; nontuberculous mycobacteria are relatively common in children and rare in adults. Objective: To identify and establish the frequency of infectious etiology by nontuberculous mycobacteria in Mexican adult patients with cervical lymphadenopathy. Methods: The study included 85 patients over 18 years with cervical lymphadenopathy; 45 were HIV-positive, 40 were HIV-negative; they had no history of tuberculosis treatment and were selected from a third-level hospital. It was carried out a biopsy of the lymph node for the histopathological study, a search for acid-fast bacilli, a tube culture to indicate growth of Mycobacterium BACTEC (MGIT-960) and identification of mycobacterial strain by PCR-RFLP (restriction fragment length polymorfism) of hsp65. Results: In 42 HIV-positive patients (93%), strains corresponded to Mycobacterium tuberculosis complex, two (4.4%) to M. intracellulare and one (2.2%) to M. gordonae. Among HIV-negative patients, 39 of strains (97.5%) corresponded to patients with M. tuberculosis complex and one strain (2.5%) to M. fortuitum. Conclusion: The presence of nontuberculous mycobacteria was found in 4.7% of all cases. Despite this low frequency, it must be taken into account as a possible cause of lymphadenopathy, since its prompt identification enables introducing specific treatment.

Introducción: la tuberculosis es un problema de salud pública mundial, sobre todo en países emergentes. El Mycobacterium tuberculosis es el principal causante de las adenopatías cervicales; las micobacterias no tuberculosas son relativamente frecuentes en el niño y raras en adultos. Objetivo: identificar y establecer la frecuencia de la etiología infecciosa por micobacterias no tuberculosas (MNT) en pacientes adultos mexicanos con linfadenopatias cervicales. Métodos: se estudiaron 85 pacientes mayores de 18 años, con linfadenopatía cervical, 45 con positividad al virus de la inmunodeficiencia humana (VIH) y 40 VIH negativos, sin antecedentes de tratamiento antituberculoso, seleccionados en un hospital de concentración de especialidad de tercer nivel. Se realizó biopsia de nodo linfático para su estudio histopatológico, búsqueda de bacilos ácido-alcohol resistentes, cultivo en el tubo indicador del crecimiento de Mycobacterium BACTEC (MGIT-960) y la identificación de cepa micobacteriana por PCR-RFLP (restriction fragment lenght polymorfism) de hsp65. Resultados: las cepas correspondieron al complejo Mycobacterium tuberculosis en 42 pacientes VIH positivos (93%), dos (4.4%) a M. intracellulare y una (2.2%) a M. gordonae. Las cepas correspondieron al complejo M. tuberculosis en 39 pacientes VIH negativos (97.5%) y una a M. fortuitum (2.5%). Conclusión: la presencia de MNT se encontró en 4.7% de todos los casos. A pesar de su baja frecuencia, deben ser tomadas en cuenta como posible causa de linfadenopatías, porque su identificación oportuna permite instaurar un tratamiento específico.

Mycobacterium kumamotonense in the cervical region in an immunocompetent patient, clinical case report in Mexico.

Non-tuberculous mycobacterial infection has increased significantly in recent years, especially in emerging countries. We present the case of a 25-year-old male patient, immunocompetent, with cervical lymphadenopathy, identifying Mycobacterium kumamotonense, a rare species in extrapulmonary forms and with a high drug resistance index.

Identification of risk factors and diagnostic methodology in serositis by M. tuberculosis / Identificación de factores de riesgo y metodología diagnóstica en serositis por M. tuberculosis

Background: Tuberculosis is a public health problem, extrapulmonary presentations have increased, it is difficult to diagnose because of the low bacillary load. Objective: To identify risk factors and to evaluate the efficiency of diagnostic methods in pleural, meningeal, peritoneal and pericardial tuberculosis. Methods: Prospective study of cases and controls. A multiple conditional logistic regression model was used to identify risk factors. Biopsy was performed and 7 mL of fluid was extracted from the affected site, Löwestein-Jensen and MGITI960 culture, Ziehl-Neelsen staining, adenosine deaminase and endpoint PCR directed to the insertion sequence 1S6110 for M. tuberculosis were performed. Results: 116 patients were included, in 58 M. tuberculosis was confirmed by positive culture (meningeal Tb 34 cases, pleural 14, peritoneal 8, pericardial 2 cases) and 58 serositis of non-tuberculous etiology. Being a carrier of HIV and living with people infected with tuberculosis were the main risk factors OR = 3.6 and OR = 6.8. The staining had sensitivity of 25.9%, PCR of 65.5% and adenosine deaminase with 82.8% Conclusions: Conventional diagnostic methods had low efficacy, adenosine deaminase and molecular biology techniques are the most useful, in our environment these tests should be performed immediately in patients with risk factors and suspected serositis of tuberculous origin.

Introducción: la tuberculosis es un problema de salud pública, las presentaciones extrapulmonares han aumentado, siendo de difícil diagnóstico por su baja carga bacilar. Objetivo: identificar los factores de riesgo y evaluar la eficacia de los métodos diagnósticos en la tuberculosis pleural, meníngea, peritoneal y pericárdica. Métodos: estudio prospectivo de casos y controles. Se empleó un modelo de regresión logística condicional múltiple para identificar factores de riesgo. Se realizó biopsia y se extrajeron siete mL de líquido presente del sitio afectado, se realizó cultivo Löwestein-Jensen y MGITI960, tinción Ziehl-Neelsen, adenosina deaminasa y PCR en punto final dirigida a la secuencia de inserción 1S6110 para M. tuberculosis. Resultados: se incluyeron 116 pacientes, en 58 se confirmó M. tuberculosis por cultivo positivo (Tb meníngea 34 casos, pleural 14, peritoneal 8, pericárdica 2 casos) y 58 serositis de etiología no tuberculosa. Ser portador de VIH y convivir con personas infectadas con tuberculosis fueron los mayores factores de riesgo OR = 3.6 y OR = 6.8. La tinción tuvo sensibilidad de 25.9%, PCR de 65.5% y adenosina deaminasa con 82.8%. Conclusiones: los métodos diagnósticos convencionales tuvieron baja eficacia, la adenosina deaminasa y las técnicas de biología molecular son los de mayor utilidad, en nuestro medio estos estudios deben realizarse de inmediato en pacientes con factores de riesgo y sospecha de serositis de origen tuberculoso.

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

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.

EV-D68 infection in children with asthma exacerbation and pneumonia in Mexico City during 2014 autumn.

BACKGROUND: Human enterovirus D68 (EV-D68) recently caused an increase in mild-to-severe pediatric respiratory cases in North America and some European countries. Even though few of these children presented with acute paralytic disease, direct causal relationship cannot yet be assumed. OBJECTIVES: The purposes of this report were to describe the clinical findings of an outbreak of EV-D68 infection in Mexico City and identify the genetic relationship with previously reported strains. PATIENTS/METHODS: Between September and December 2014, 126 nasopharyngeal samples (NPS) of hospitalized children <15 years of age with ARI were tested for the presence of respiratory viruses using a multiplex RT-qPCR and EV-D68-specific RT-qPCR. Clinical, epidemiological, and demographic data were collected and associated with symptomatology and viral infections. Phylogenetic analyses were performed using VP1 region. RESULTS: Enterovirus/rhinovirus infection was detected in 40 patients (31·7%), of which 24 patients were EV-D68-positive. EV-D68 infection prevailed over September and October 2014 and was associated with neutrophilia and lymphopenia, and patients were more likely to develop hypoxemia. Phylogenetic analyses showed that Mexican EV-D68 belongs to the new B1 clade. CONCLUSIONS: This is the first EV-D68 outbreak described in Mexico and occurred few weeks after the United States reported similar infections. Although EV-D68 belongs to new B1 clade, no neurological affection was observed.

Fatal Psychrobacter sp. infection in a pediatric patient with meningitis identified by metagenomic next-generation sequencing in cerebrospinal fluid.

The genus Psychrobacter contains environmental, psychrophilic and halotolerant gram-negative bacteria considered rare opportunistic pathogens in humans. Metagenomics was performed on the cerebrospinal fluid (CSF) of a pediatric patient with meningitis. Nucleic acids were extracted, randomly amplified, and sequenced with the 454 GS FLX Titanium next-generation sequencing (NGS) system. Sequencing reads were assembled, and potential virulence genes were predicted. Phylogenomic and phylogenetic studies were performed. Psychrobacter sp. 310 was identified, and several virulence genes characteristic of pathogenic bacteria were found. The phylogenomic study and 16S rRNA gene phylogenetic analysis showed that the closest relative of Psychrobacter sp. 310 was Psychrobacter sanguinis. To our knowledge, this is the first report of a meningitis case associated with Psychrobacter sp. identified by NGS metagenomics in CSF from a pediatric patient. The metagenomic strategy based on NGS was a powerful tool to identify a rare unknown pathogen in a clinical case.

Hsp65 phylogenetic assay for molecular diagnosis of nontuberculous mycobacteria isolated in Mexico.

BACKGROUND AND AIMS: Nontuberculous mycobacteria (NTM) are mainly distributed as important emerging pathogens in patients with chronic or immunosuppressive diseases. Accurate identification of causative species is crucial for proper treatment and patient follow-up. However, several difficulties are associated with phenotypic and molecular diagnostic methods for precise identification at the species level due to shared metabolic and genetic characteristics. We undertook this study to evaluate the application of the phylogenetic method based on hsp65 gene into Telenti's PCR-restriction enzyme analysis (PRA) for molecular identification of NTM. METHODS: The study population was comprised of 1646 Mycobacterium clinical isolates (AFB positive) collected from 2008-2011, of which 537 (32.6%) were MNT identified by PRA analysis. DNA sequencing of hsp65 in 53 isolates (10%) was performed. Sequence identification through NCBI-Basic Local Alignment Search Tool (BLAST) achieved correct identification in 23 isolates. Phylogenetic trees including hsp65 available GenBank sequences for all described genres of NTM and hsp65 obtained sequences were constructed using Mega 5.05 software. We compared sequence identification based on phylogenetic clustering and BLAST similarity search. RESULTS: Phylogenetic clustering allowed more specific differentiation of closely related species and clearer identification in comparison with BLAST; 30 Mycobacterium species (this is the first report of isolation of some of these from clinical samples in Mexico) were identified in this way. CONCLUSIONS: The proposed 440 bp hsp65 phylogenetic method allows a better identification tool to differentiate Mycobacterium species and is useful to complement diagnosis and epidemiological surveillance of NTM.

Detección de la Beta lactamasa de espectro OXA-141 en cepas de Pseudomonas aeruginosa aisladas de pacientes con fibrosis quística / No disponible

Introducción: Los objetivos de este trabajo fueron estudiar la presencia de -lactamasas de espectro extendido (BLEE), investigar la ubicación de los genes que codifican para esas enzimas y determinar la relación clonal de cepas de Pseudomonas aeruginosa resistentes a la ceftazidima aisladas de pacientes mexicanos con fibrosis quística. Metodología: Se determinó el perfil de resistencia a 11 antibióticos (CLSI) y la detección fenotípica de las BLEE siguiendo un método de difusión en discos de papel filtro adaptado para P. aeruginosa. La caracterización de los genes de las BLEE y de integrones se realizó por PCR y secuenciación del ADN, mientras que el análisis de la relación clonal se realizó por PFGE. Resultados: De las 148 cepas en estudio, 22 resultaron resistentes a la ceftazidima y el análisis por PCR y secuenciación reveló la presencia del genblaOXA-141 en 7 cepas, 6 resistentes y una sensible a la ceftazidima. Asimismo, blaGES se detectó en 11 cepas. Los genes intI2 e intI3 no se detectaron por PCR, pero en las 6cepas resistentes a la ceftazidima se descubrió el gen blaOXA-141 en un integrón de la clase 1. El análisis de la relación clonal de los aislamientos mostró que la mayoría de los pacientes se infectaron a lo largo del periodo de estudio con cepas de P. aeruginosa que presentaron patrones diferentes, principalmente en los individuos que no tenían relación familiar. Conclusiones: Este trabajo demuestra la existencia del gen blaOXA-141 asociado a un integrón de clase 1 en varias cepas de P. aeruginosa, así como de genes blaGES cuya localización y variante están en estudio en el grupo de investigación. Lo anterior, aunado a la diversidad de cepas capaces de infectar a individuos sensibles, sugiere un riesgo de dispersión de las cepas de P. aeruginosa productoras de BLEE entre la población mexicana que padece fibrosis quística (AU)

Introduction: The aims of this research were to study the presence of extended spectrum -lactamases(ESBL) to investigate the location of the genes encoding these enzymes, and determine the clonal relationship of strains of ceftazidime-resistant Pseudomonas aeruginosa isolated from Mexican patients with cystic fibrosis. Methods: We determined the resistance profile to 11 antibiotics (CLSI) and phenotypic ESBL detection following a disk diffusion method adapted for P. aeruginosa. Characterization of ESBL genes and integrons was performed by polymerase chain reaction (PCR) and DNA sequencing, while analysis of the clonal relationship was performed by pulsed field gel electrophoresis (PFGE) Results: Of the 148 strains studied, 22 were resistant to ceftazidime, and analysis by PCR and sequencing revealed the presence of the gene blaOXA-141 in 7 strains, 6 of which were resistant and one, susceptible to ceftazidime. In addition, blaGES was detected in 11 strains. intI2 and intI3 genes were not detected byPCR, but in the 6 ceftazidime-resistant strains, the blaOXA-141 gene was determined in a class 1 integron. Analysis of the clonal relationship of isolates showed that the majority of patients were infected during the study period with P. aeruginosa strains that exhibit different patterns, especially in individuals without a familial relationship. Conclusions: This report demonstrates the existence of the blaOXA-141 gene associated with a class 1 integron in several strains of P. aeruginosa, as well as blaGES genes, and their location and variants are being studied by our research group. This, combined with the diversity of strains able to infect several susceptible individuals, suggests the risk of spread of P. aeruginosa-strain ESBL producers among Mexican populations with cystic fibrosis (AU)

[Detection of extended spectrum ß-lactamase OXA-141 in Pseudomonas aeruginosa strains isolated from patients with cystic fibrosis]. / Detección de la ß-lactamasa de espectro extendido OXA-141 en cepas de Pseudomonas aeruginosa aisladas de pacientes con fibrosis quística.

INTRODUCTION: The aims of this research were to study the presence of extended spectrum ß-lactamases (ESBL) to investigate the location of the genes encoding these enzymes, and determine the clonal relationship of strains of ceftazidime-resistant Pseudomonas aeruginosa isolated from Mexican patients with cystic fibrosis. METHODS: We determined the resistance profile to 11 antibiotics (CLSI) and phenotypic ESBL detection following a disk diffusion method adapted for P. aeruginosa. Characterization of ESBL genes and integrons was performed by polymerase chain reaction (PCR) and DNA sequencing, while analysis of the clonal relationship was performed by pulsed field gel electrophoresis (PFGE). RESULTS: Of the 148 strains studied, 22 were resistant to ceftazidime, and analysis by PCR and sequencing revealed the presence of the gene bla(OXA-141) in 7 strains, 6 of which were resistant and one, susceptible to ceftazidime. In addition, bla(GES) was detected in 11 strains. intI2 and intI3 genes were not detected by PCR, but in the 6 ceftazidime-resistant strains, the bla(OXA-141) gene was determined in a class 1 integron. Analysis of the clonal relationship of isolates showed that the majority of patients were infected during the study period with P. aeruginosa strains that exhibit different patterns, especially in individuals without a familial relationship. CONCLUSIONS: This report demonstrates the existence of the bla(OXA-141) gene associated with a class 1 integron in several strains of P. aeruginosa, as well as bla(GES) genes, and their location and variants are being studied by our research group. This, combined with the diversity of strains able to infect several susceptible individuals, suggests the risk of spread of P. aeruginosa-strain ESBL producers among Mexican populations with cystic fibrosis.