RESUMEN
OBJECTIVES: To determine genomic characteristics and molecular epidemiology of carbapenem non-susceptible Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa from medical centres of Mexico using whole genome sequencing data analysed with the EPISEQâ CS application and other bioinformatic platforms. METHODS: Clinical isolates collected from 28 centres in Mexico included carbapenem-non-susceptible K. pneumoniae (n = 22), E. coli (n = 24), A. baumannii (n = 16), and P. aeruginosa (n = 13). Isolates were subjected to whole genome sequencing using the Illumina (MiSeq) platform. FASTQ files were uploaded to the EPISEQâ CS application for analysis. Additionally, the tools Kleborate v2.0.4 and Pathogenwatch were used as comparators for Klebsiella genomes, and the bacterial whole genome sequence typing database was used for E. coli and A. baumannii. RESULTS: For K. pneumoniae, both bioinformatic approaches detected multiple genes encoding aminoglycoside, quinolone, and phenicol resistance, and the presence of blaNDM-1 explained carbapenem non-susceptibility in 18 strains and blaKPC-3 in four strains. Regarding E. coli, both EPISEQâ CS and bacterial whole genome sequence typing database analyses detected multiple virulence and resistance genes: 20 of 24 (83.3%) strains carried blaNDM, 3 of 24 (12.4%) carried blaOXA-232, and 1 carried blaOXA-181. Genes that confer resistance to aminoglycosides, tetracyclines, sulfonamides, phenicols, trimethoprim, and macrolides were also detected by both platforms. Regarding A. baumannii, the most frequent carbapenemase-encoding gene detected by both platforms was blaOXA-72, followed by blaOXA-66. Both approaches detected similar genes for aminoglycosides, carbapenems, tetracyclines, phenicols, and sulfonamides. Regarding P. aeruginosa, blaVIM, blaIMP, and blaGES were the more frequently detected. Multiple virulence genes were detected in all strains. CONCLUSION: Compared to the other available platforms, EPISEQâ CS enabled a comprehensive resistance and virulence analysis, providing a reliable method for bacterial strain typing and characterization of the virulome and resistome.
Asunto(s)
Antibacterianos , Escherichia coli , Escherichia coli/genética , Antibacterianos/farmacología , Antibacterianos/uso terapéutico , Bacterias Gramnegativas , Carbapenémicos , Klebsiella pneumoniae , Aminoglicósidos , Pseudomonas aeruginosa/genética , Biología ComputacionalRESUMEN
OBJECTIVE: To describe the clinical and molecular characteristics of methicillin-resistant Staphylococcus aureus (MRSA) strains that were collected in the Hospital Regional de Alta Especialidad de Veracruz (HRV). MATERIALS AND METHODS: A total of 107 MRSA strains from individual patients were examined. The strains were collected between September 2009 and September 2010. The clinical and demographic characteristics of patients were analyzed; molecular typing by pulsed-field gel electrophoresis (PFGE), staphylococcal chromosomal cassette mec (SCCmec) typing and multilocus sequence typing were used to characterize the isolates. RESULTS: Two PFGE patterns (NY/J and IB) were identified with 4 and 3 subtypes respectively. The isolates analyzed showed two SCCmec types (I and II) and two sequence types (ST): ST247 and ST5 related with the Iberian and New York/Japan clones respectively. CONCLUSIONS: This study establishes the presence of two very important clonal lineages of MRSA: New York/Japan and Iberian clone in the hospital environment.
OBJETIVO: Describir las características clínicas y moleculares de cepas de Staphylococcus aureus resistentes a meticilina (SARM) que fueron recolectadas en el Hospital Regional de Alta Especialidad de Veracruz (HRV). MATERIAL Y MÉTODOS: Un total de 107 cepas de SARM fueron analizadas en el presente estudio. Las cepas estudiadas fueron recolectadas de septiembre de 2009 a septiembre de 2010. Las características clínicas y demográficas de los pacientes fueron analizadas; la tipificación molecular de las cepas se hizo por electroforesis en campos pulsados, casete cromosomal estafilococócico (SCCmec, en inglés) y secuenciación de múltiples locus. RESULTADOS: Dos patrones electroforéticos (NY/J y IB) fueron identificados con 4 y 3 subtipos respectivamente. Los aislamientos analizados mostraron dos tipos de SCCmec (I y II) y dos secuencias tipo (ST): ST247 y ST5 relacionados con las clonas Ibérica y Nueva York/Japón respectivamente. CONCLUSIONES: . Este estudio estableció la presencia en el medio hospitalario de dos linajes clonales de SARM importantes: Nueva York/Japón e Ibérico.
Asunto(s)
Staphylococcus aureus Resistente a Meticilina/aislamiento & purificación , Hospitales , MéxicoRESUMEN
Abstract: Objective: To describe the clinical and molecular characteristics of methicillin-resistantStaphylococcus aureus(MRSA) strains that were collected in theHospital Regional de Alta Especialidad de Veracruz(HRV). Materials and methods: A total of 107 MRSA strains from individual patients were examined. The strains were collected between September 2009 and September 2010. The clinical and demographic characteristics of patients were analyzed; molecular typing by pulsed-field gel electrophoresis (PFGE), staphylococcal chromosomal cassette mec (SCCmec) typing and multilocus sequence typing were used to characterize the isolates. Results: Two PFGE patterns (NY/J and IB) were identified with 4 and 3 subtypes respectively. The isolates analyzed showed two SCCmec types (I and II) and two sequence types (ST): ST247 and ST5 related with the Iberian and New York/Japan clones respectively. Conclusion: This study establishes the presence of two very important clonal lineages of MRSA: New York/Japan and Iberian clone in the hospital environment.
Resumen: Objetivo: Describir las características clínicas y moleculares de cepas deStaphylococcus aureusresistentes a meticilina (SARM) que fueron recolectadas en el Hospital Regional de Alta Especialidad de Veracruz (HRV). Material y métodos: Un total de 107 cepas de SARM fueron analizadas en el presente estudio. Las cepas estudiadas fueron recolectadas de septiembre de 2009 a septiembre de 2010. Las características clínicas y demográficas de los pacientes fueron analizadas; la tipificación molecular de las cepas se hizo por electroforesis en campos pulsados, casete cromosomal estafilococócico (SCCmec, en inglés) y secuenciación de múltiples locus. Resultados: Dos patrones electroforéticos (NY/J y IB) fueron identificados con 4 y 3 subtipos respectivamente. Los aislamientos analizados mostraron dos tipos de SCCmec (I y II) y dos secuencias tipo (ST): ST247 y ST5 relacionados con las clonas Ibérica y Nueva York/Japón respectivamente. Conclusión: Este estudio estableció la presencia en el medio hospitalario de dos linajes clonales de SARM importantes: Nueva York/Japón e Ibérico.
