First report and comparative genomics analysis of a blaoxa-244-haarboring escherichia coli isolate recovered in the American continent

The carbapenemase OXA-244 is a derivate of OXA-48, and its detection is very difficult in laboratories. Here, we report the identification and genomic analysis of an Escherichia coli isolate (28Eco12) harboring the blaOXA-244 gene identified in Colombia, South America. The 28Eco12 isolate was identified during a retrospective study, and it was recovered from a patient treated in Colombia. The complete nucleotide sequence was established using the PacBio platform. A comparative genomics analysis with other blaOXA-244–harboring Escherichia coli strains was performed. The 28Eco12 isolate belonged to sequence type (ST) 38, and its genome was composed of two molecules, a chromosome of 5,343,367 bp and a plasmid of 92,027 bp, which belonged to the incompatibility group IncY and did not harbor resistance genes. The blaOXA-244 gene was chromosomally encoded and mobilized by an ISR1-related Tn6237 composite transposon. Notably, this transposon was inserted and located within a new genomic island. To our knowledge, this is the first report of a blaOXA-244–harboring Escherichia coli isolate in America. Our results suggest that the introduction of the OXA-244-producing E. coli isolate was through clonal expansion of the ST38 pandemic clone. Other isolates producing OXA-244 could be circulating silently in America

Diseño de dos metodologías moleculares para la rápida identificación de aislamientos de Staphylococcus aureus resistente a meticilina asociados a la comunidad en Colombia

Introduction. Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) infections are found with increasing the frequency, both in healthy individuals in the community and in hospitalized patients. In Colombia and the Andean region, CA-MRSA isolates have a genetic background that is related to the pandemic USA300 clone.Objective. Two molecular methods are designed and standardized for the rapid differentiation of Colombian community-acquired and hospital-acquired methicillin-resistant Staphylococcus aureus (HA-MRSA) isolates.Materials and methods. Two molecular methods were standardized for the identification of CA-MRSA isolates. The first method was based on the differential digestion of the carbamate kinase (arcC) and guanylate kinase (gmk) genes in the sequences type 5 (ST5) in the HA-MRSA isolates and 8 (ST8) in the CA-MRSA isolates. The second method was based on the PCR amplification of 5 specific virulence factors found in CA-MRSA and HA-MRSA isolates. The specificity and precision of each method wereevaluated using 237 clinical MRSA isolates.Results. The first method identified 100% and 93.2% of the CA-MRSA and HA-MRSA isolates, respectively. The second method also correctly identified the two isolates types (CA-MRSA and HAMRSA).Conclusions. These two methods are a convenient alternative for the rapid identification of the CAMRSA isolates, compared with other techniques such as pulsed field gel electrophoresis and multilocus sequence typing, which are time-consuming and more expensive.Introducción. Los aislamientos de Staphylococcus aureus resistente a la meticilina asociado a la comunidad (SARM-AC), están aumentando la frecuencia de infecciones en personas sanas de la comunidad y en pacientes hospitalizados. En Colombia y en la región andina estos aislamientos tienen un componente genético relacionado con el clon pandémico USA300.Objetivo. Diseñar y estandarizar dos metodologías para la diferenciación rápida de aislamientos colombianos de S. aureus resistente a la meticilina asociado a la comunidad de los asociados al hospital (SARM-AH).Materiales y métodos. Se estandarizaron dos metodologías moleculares para la identificación de aislamientos de S. aureus resistente a la meticilina asociado a la comunidad. La primera se basa en la digestión diferencial con tres enzimas de restricción de los genes cinasa de carbamato (arcC) y cinasa de guanilato (gmk) para los tipos de secuencia 5 (ST5) y 8 (ST8), correspondientes a aislamientos de S. aureus resistente a la meticilina asociado al hospital y asociado a la comunidad, respectivamente. La segunda se basa en la amplificación por reacción en cadena de la polimerasa de cinco factores de virulencia que se encuentran de manera diferencial en estos aislamientos. Las dos metodologías fueron validadas en 237 aislamientos clínicos de S. aureus resistente a la meticilina.Resultados. Con la primera metodología se identificaron el 100 % y 93,2 % de los aislamientos de S. aureus resistente a la meticilina asociado a la comunidad y asociado al hospital, respectivamente. Con la segunda metodología se identificaron correctamente los dos tipos de aislamientos.Conclusiones. Estas dos metodologías son una buena alternativa en términos de ahorro en tiempo y dinero comparadas con otras técnicas, como la electroforesis en campo pulsado y la tipificación de secuencias multilocus para la rápida identificación de aislamientos de S. aureus resistente a la meticilina asociado a la comunidad en Colombia. doi: http://dx.doi.org/10.7705/biomedica.v32i2.645

Neumonía necrosante por Staphylococcus aureus extrahospitalario resistente a la meticilina:reporte de dos casos en Colombia

The emergence of community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) as a cause of severe infections has been described in the recent years. In 2006, the first report of skin and soft tissue infection by CA-MRSA was published in Colombia. Herein, two additional cases of CA-MRSA are reported with a clinical course characterized by rapid progression, prolonged stay in the intensive care unit and complication of pneumonia with the onset of empyema. Both adult patients developed acute renal failure, and were treated with linezolide; the subsequent clinical response showed adequate treatment response. Molecular characterization of the isolates indicated the presence of the mecA gene carrying the cassette SCCmec type IV and the production of the toxin panton-valentine leukocidin.En los últimos años se ha informado la aparición de Staphylococcus aureus resistente a la meticilina como causa de infecciones extrahospitalarias graves. En Colombia, en el 2006, se publicó el primer reporte de S. aureus como causa de infección de piel y tejidos blandos; en esta ocasión, presentamos el primer reporte de neumonía necrosante con etiología por S. aureus, en dos pacientes adultos que se caracterizaron por presentar progresión clínica rápida, estancia prolongada en cuidados intensivos y complicación de la neumonía con aparición de empiema.Ambos desarrollaron falla renal aguda, por lo que fueron manejados con linezolide, con adecuada respuesta clínica. Con la caracterización molecular de los aislamientos se confirmó la presencia del gen mecA que porta el casete SCCmec tipo IV y la producción de la toxina leucocidina Panton-Valentine

Control de la diferenciación en células de la eritroleucemia murina análisis de la expresión diferencial de la proteína ribosómica S5, RAN/TC4 u CLK/STY

Tesis doctoral inédita leida en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología Molecular. Fecha de lectura: 10-06-199

Diseño de dos metodologías moleculares para la rápida identificación de aislamientos de Staphylococcus aureus resistente a meticilina asociados a la comunidad en Colombia

Introducción. Los aislamientos de Staphylococcus aureus resistente a la meticilina asociado a la comunidad (SARM-AC), están aumentando la frecuencia de infecciones en personas sanas de la comunidad y en pacientes hospitalizados. En Colombia y en la región andina estos aislamientos tienen un componente genético relacionado con el clon pandémico USA300. Objetivo. Diseñar y estandarizar dos metodologías para la diferenciación rápida de aislamientos colombianos de S. aureus resistente a la meticilina asociado a la comunidad de los asociados al hospital (SARM-AH). Materiales y métodos. Se estandarizaron dos metodologías moleculares para la identificación de aislamientos de S. aureus resistente a la meticilina asociado a la comunidad. La primera se basa en la digestión diferencial con tres enzimas de restricción de los genes cinasa de carbamato (arcC) y cinasa de guanilato (gmk) para los tipos de secuencia 5 (ST5) y 8 (ST8), correspondientes a aislamientos de S. aureus resistente a la meticilina asociado al hospital y asociado a la comunidad, respectivamente. La segunda se basa en la amplificación por reacción en cadena de la polimerasa de cinco factores de virulencia que se encuentran de manera diferencial en estos aislamientos. Las dos metodologías fueron validadas en 237 aislamientos clínicos de S. aureus resistente a la meticilina. Resultados. Con la primera metodología se identificaron el 100 % y 93,2 % de los aislamientos de S. aureus resistente a la meticilina asociado a la comunidad y asociado al hospital, respectivamente. Con la segunda metodología se identificaron correctamente los dos tipos de aislamientos. Conclusiones. Estas dos metodologías son una buena alternativa en términos de ahorro en tiempo y dinero comparadas con otras técnicas, como la electroforesis en campo pulsado y la tipificación de secuencias multilocus para la rápida identificación de aislamientos de S. aureus resistente a la meticilina asociado a la comunidad en Colombia.   doi: http://dx.doi.org/10.7705/biomedica.v32i2.64

First Report and Comparative Genomics Analysis of a blaOXA-244-Harboring Escherichia coli Isolate Recovered in the American Continent

The carbapenemase OXA-244 is a derivate of OXA-48, and its detection is very difficult in laboratories. Here, we report the identification and genomic analysis of an Escherichia coli isolate (28Eco12) harboring the blaOXA-244 gene identified in Colombia, South America. The 28Eco12 isolate was identified during a retrospective study, and it was recovered from a patient treated in Colombia. The complete nucleotide sequence was established using the PacBio platform. A comparative genomics analysis with other blaOXA-244–harboring Escherichia coli strains was performed. The 28Eco12 isolate belonged to sequence type (ST) 38, and its genome was composed of two molecules, a chromosome of 5,343,367 bp and a plasmid of 92,027 bp, which belonged to the incompatibility group IncY and did not harbor resistance genes. The blaOXA-244 gene was chromosomally encoded and mobilized by an ISR1-related Tn6237 composite transposon. Notably, this transposon was inserted and located within a new genomic island. To our knowledge, this is the first report of a blaOXA-244–harboring Escherichia coli isolate in America. Our results suggest that the introduction of the OXA-244-producing E. coli isolate was through clonal expansion of the ST38 pandemic clone. Other isolates producing OXA-244 could be circulating silently in America

Epidemiología molecular y caracterización de genes de virulencia de aislados de estafilococo aureus resistentes a la meticilina adquiridos en la comunidad y adquiridos en el hospital en Colombia

Objective: To determine the molecular epidemiology and presence of virulence genes in communityacquired (CA) and hospital-acquired (HA) methicillin-resistant Staphylococcus aureus (MRSA) isolates and their relationship to clinical outcomes. Methods: An observational and prospective study of infections caused by MRSA was conducted between June 2006 and December 2007 across seven hospitals in three Colombian cities. MRSA isolates were analyzed for SCCmec. Also, pulsed-field gel electrophoresis and multilocus sequence typing were performed and 25 virulence genes were identified. Results: Two hundred and seventy isolates were collected from 262 adult hospital patients with MRSA infections. Overall, 68% of the isolates were classified as HA-MRSA and 32% as CA-MRSA. We identified differences in the patterns of virulence genes: 85% of HA-MRSA isolates possessed the enterotoxin gene cluster (egc), whereas 92% of CA-MRSA isolates possessed the lukF-PV/lukS-PV genes. Multivariate analysis showed an increased risk of mortality for seg (p = 0.001, odds ratio 4.73) and a protective effect for eta (p = 0.018, odds ratio 0.33). Conclusions: Our study confirms that three clones of MRSA predominantly circulate in Colombia: a Chilean clone, a pediatric clone that causes HA-MRSA infections, and a USA300-related clone (SCCmec IVc) in CA-MRSA infections, which differ in the content of clinically important virulence genes. This study confirms that PVL is not a determinant of severity or mortality in CA-MRSA infections. 2013 International Society for Infectious Diseases. Published by Elsevier Ltd. All rights reserved

Epidemiología molecular y caracterización de genes de virulencia de aislados de estafilococo aureus resistentes a la meticilina adquiridos en la comunidad y adquiridos en el hospital en Colombia

Objective: To determine the molecular epidemiology and presence of virulence genes in communityacquired (CA) and hospital-acquired (HA) methicillin-resistant Staphylococcus aureus (MRSA) isolates and their relationship to clinical outcomes. Methods: An observational and prospective study of infections caused by MRSA was conducted between June 2006 and December 2007 across seven hospitals in three Colombian cities. MRSA isolates were analyzed for SCCmec. Also, pulsed-field gel electrophoresis and multilocus sequence typing were performed and 25 virulence genes were identified. Results: Two hundred and seventy isolates were collected from 262 adult hospital patients with MRSA infections. Overall, 68% of the isolates were classified as HA-MRSA and 32% as CA-MRSA. We identified differences in the patterns of virulence genes: 85% of HA-MRSA isolates possessed the enterotoxin gene cluster (egc), whereas 92% of CA-MRSA isolates possessed the lukF-PV/lukS-PV genes. Multivariate analysis showed an increased risk of mortality for seg (p = 0.001, odds ratio 4.73) and a protective effect for eta (p = 0.018, odds ratio 0.33). Conclusions: Our study confirms that three clones of MRSA predominantly circulate in Colombia: a Chilean clone, a pediatric clone that causes HA-MRSA infections, and a USA300-related clone (SCCmec IVc) in CA-MRSA infections, which differ in the content of clinically important virulence genes. This study confirms that PVL is not a determinant of severity or mortality in CA-MRSA infections. 2013 International Society for Infectious Diseases. Published by Elsevier Ltd. All rights reserved

Caracterización genética y molecular de Pseudomonas Aeruginosa causante de infecciones en UCI de tres ciudades de Colombia.

Pseudomonas aeruginosa, ubiquitous bacteria that can generate complicated infections in hospital patients, increasing morbidity and mortality rates due to increased antimicrobial resistance in clinical use, especially the last therapeutic option as carbapenems for the acquisition of resistance determinants through mainly mobile genetic elements.OBJECTIVE: To characterize the resistance profile and molecular characteristics of P. aeruginosa isolated from adult patients with a diagnosis of infection in three intensive care units in Colombia. METHODS: Patients with P. aeruginosa infections in adults were analyzed UCI. A bacterial isolates were determined profile of susceptibility to 12 antibiotics and resistance genes were amplified β-lactams, quinolones, sulfonamides and genetic platforms like integron class 1 and 2. The genetic relationship by PFGE and MLST. RESULTS: In the study 40 patients of which 23 (57.5%) analyzed belong to an ICU in the city of Pereira. The main sources of isolating microorganisms are 13 blood cultures (32.5%) and urine-11 (27.5%). Resistance profiles SAM-SAM-FOX and FOX-SXT occurred in 6 (15.0%) and 4 (10.0%) isolates respectively. The β-lactamases frequently were blaTEM type in 8 (20.0%), blaSHV seven (17.5%) and blaCTX-M 3 (7.5%), carbapenemases blaVIM blaKPC-2 and type 4 (9.7%) and 3 (7.5%). Isolates presented a polyclonal behavior pulsotypes 28. The KPC-producing isolates 2 and VIM are associated with the ST235 and ST111 respectively. CONCLUSION: those generated in ICUs participating entities infections are highly variable and moderate resistance to carbapenems associated with the presence of KPC-2 and VIM associated with the pandemic clone ST235 and ST111.Pseudomonas aeruginosa, bacteria ubicua que puede generar infecciones complicadas en pacientes hospitalarios, incrementando los índices de morbimortalidad debido al incremento de resistencia a los antimicrobianos de uso clínico, en especial los de última opción terapéutica como los carbapenémicos por la adquisición de determinantes de resistencia a través de elementos genéticos móviles principalmente. OBJETIVO: Caracterizar el perfil de resistencia y características moleculares de P. aeruginosa, aislada de pacientes adultos con diagnóstico de infección en tres unidades de cuidados intensivos en Colombia.MÉTODOS: Se analizaron pacientes con infecciones por P.aeruginosa en UCI adultos. A los aislamientos bacterianos se les determinó el perfil de susceptibilidad a 12 antibióticos y se amplificaron genes de resistencia a β-lactámicos, quinolonas, sulfonamidas y plataformas genéticas como integrón clase 1 y 2. La relación genética por medio de PFGE y MLST. RESULTADOS: En el estudio se analizaron 40 pacientes de los cuales 23(57,5%) pertenecen a una UCI en la ciudad de Pereira. Las principales fuentes de aislamiento de los microorganismos son hemocultivos 13(32,5%) y urocultivos 11(27,5%). Los perfiles de resistencia SAM-FOX y SAM-FOX-SXT se presentaron en 6(15,0%) y 4(10,0%) aislamientos respectivamente. Las β-lactamasas más frecuentes fueron de tipo blaTEM, en 8(20,0%), blaSHV 7(17.5%) y blaCTX-M 3(7.5%), carbapenemasas de tipo blaKPC-2 y blaVIM en 4(9.7%) y 3(7.5%). Los aislamientos presentan un comportamiento policlonal con 28 pulsotipos. Los aislamientos productores de KPC-2 y VIM se encuentran asociados al ST235 y ST111 respectivamente. CONCLUSIONES: las infecciones generadas en las UCI de las entidades participantes presentan gran variabilidad y con una moderada resistencia a carbapenémicos asociados a la presencia de KPC-2 y VIM asociados al clon pandémico ST235 y ST111

Outbreak of NDM-1-producing Klebsiella pneumoniae in a neonatal unit in Colombia

Six multiresistant, NDM-1-producing Klebsiella pneumoniae strains were recovered from an outbreak that affected six neonatal patients in a Colombian hospital. Molecular analysis showed that all of the isolates harbored the blaNDM-1, qnrA, and intI1 genes and were clonally related. Multilocus sequence typing showed that the isolates belonged to a new sequence type (ST1043) that was different from the sequence types that had previously been reported. This is the first report of NDM-1-producing isolates in South America