Comparative genomics of global optrA-carrying Enterococcus faecalis uncovers a common chromosomal hotspot for optrA acquisition within a diversity of core and accessory genomes

Freitas, Ana R.; Tedim, Ana P.; Novais, Carla; Lanza, Val F.; Peixe, Luı́sa

doi:10.1099/mgen.0.000350

Cited by 40 publications

(49 citation statements)

References 74 publications

(129 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

Section: Discussionunclassified

“…Las variantes optrA -2, optrA -5 y opt r A -6 identificadas en este estudio han sido reportadas en humanos ( 4 , 7 , 8 , 14 , 21 ) y alimentos de origen animal ( 18 , 19 , 21 ); optrA -2 se ha identificado incluso en aguas residuales ( 18 , 21 ). En Colombia, optrA -2 se ha descrito previamente en carne cruda ( 16 , 21 ), mientras que es la primera vez que se reporta optrA 5 y optrA -6. La variante más común fue optrA -2 (EDM) y aunque ninguno de estos aislamientos presentó mecanismos adicionales de resistencia al linezolid, todos fueron resistentes al linezolid con CIM entre 8 y >256 µg/mL, contrastando con los datos publicados por Cai y cols ( 14 ) donde aislamientos optrA -2 (EDM) presentaron una CIM al linezolid en el rango sensible e intermedio (=2 y 4 µg/mL, respectivamente); el estudio de Cai y cols.…”

Section: Discussionunclassified

“…Así mismo, se han identificado microorganismos portadores del gen optrA en alimentos de origen animal ( 11 , 16 - 18 ), personas hospitalizadas e individuos sanos ( 4 , 7 , 11 - 14 ), aguas residuales ( 19 ) y suelos ( 20 ). Este gen ha sido detectado en diferentes plásmidos y cromosomas ( 4 , 11 , 13 - 21 ). Actualmente optrA se ha reportado en países de Asia ( 4 , 14 , 15 , 19 , 21 ), Europa ( 4 , 8 , 17 , 22 - 24 ), África ( 18 , 19 , 21 ) y América ( 4 , 16 , 21 ).…”

unclassified

“…Este gen ha sido detectado en diferentes plásmidos y cromosomas ( 4 , 11 , 13 - 21 ). Actualmente optrA se ha reportado en países de Asia ( 4 , 14 , 15 , 19 , 21 ), Europa ( 4 , 8 , 17 , 22 - 24 ), África ( 18 , 19 , 21 ) y América ( 4 , 16 , 21 ). En Colombia, la primera detección de optrA se realizó en Enterococcus faecalis recuperados en carne cruda de origen avícola ( 16 ).…”

unclassified

See 3 more Smart Citations

Vigilancia nacional de aislamientos clínicos de Enterococcus faecalis resistentes al linezolid portadores del gen optrA en Colombia, 2014-2019

Saavedra

Bernal

Montilla-Escudero

et al. 2020

Revista Panamericana De Salud Pública

View full text Add to dashboard Cite

Objetivo. Describir las características epidemiológicas, fenotípicas y genéticas de aislamientos clínicos portadores de optrA identificados en la vigilancia de resistencia antimicrobiana por el laboratorio del Instituto Nacional de Salud de Colombia. Métodos. Entre octubre de 2014 y febrero 2019, se recibieron 25 aislamientos de Enterococcus spp. resistentes al linezolid. La identificación y sensibilidad antimicrobiana se determinó con Vitek 2 y la concentración inhibitoria mínima (CIM) al linezolid se estableció con E-test. El gen optrA se detectó mediante PCR. La diversidad genética de aislamientos positivos para optrA se analizó con Diversilab®. Se seleccionaron seis aislamientos para llevar a cabo la secuenciación del genoma completo. Resultados. Se confirmó el gen optrA en 23/25 aislamientos de E. faecalis de siete departamentos de Colombia. Los aislamientos presentaron una CIM al linezolid entre 8 y >256µg/mL. La tipificación por Diversilab® indicó una amplia variabilidad genética. Todos los aislamientos analizados mediante secuenciación del genoma completo, presentaron genes de resistencia fexA, ermB, lsaA, tet(M), tet(L) y dfrG además de optrA y fueron negativos para otros mecanismos de resistencia al linezolid. Se identificaron tres secuencias tipos y tres variantes de optrA: ST16 (optrA-2), ST476 (optrA-5) y ST618 (optrA-6). El entorno genético de los aislamientos optrA-2 (ST16) presentó el segmento impB, fex, optrA, asociado a plásmido, mientras que en dos aislamientos (optrA-6 y optrA-5) se encontró el elemento cromosómico transferible Tn6674-like. Conclusión. Los aislamientos clínicos positivos para optrA presentan una alta diversidad genética, con diferentes clones y variantes de optrA relacionados con dos tipos de estructuras y diferentes elementos genéticos móviles.

show abstract

Section: Discussionunclassified

unclassified

See 2 more Smart Citations

Vigilancia nacional de aislamientos clínicos de Enterococcus faecalis resistentes al linezolid portadores del gen optrA en Colombia, 2014-2019

Saavedra

Bernal

Montilla-Escudero

et al. 2020

Revista Panamericana De Salud Pública

View full text Add to dashboard Cite

show abstract

“…We evaluated all 17 E. faecalis genomes for the presence of virulence-associated genes and operons using the VirulenceFinder database (33), along with manually searches for putative virulence gene sequences that have been previously described in E. faecalis (34) (Table S4). We found that fibronectin-binding proteins efbA and efaAfs, endocarditis and biofilm-associated pili ebpABC, sortase A (srtA), adhesin to collagen of E. faecalis (ace), general stress proteins gls24 and glsB, membrane metalloprotease associated with endocarditis (eep), thiol peroxidase for oxidative stress resistance (tpx), and sex pheromones cCF10, cOB1, cad and camE were present in the genomes of all isolates, with variable nucleotide identity (97-100% versus the reference sequence).…”

Section: Virulence-associated Gene Profiles and Biofilm Formationmentioning

confidence: 99%

Genomic and phenotypic diversity ofEnterococcus faecalisisolated from endophthalmitis

Chilambi

Nordstrom

Evans

et al. 2020

Preprint

View full text Add to dashboard Cite

Enterococcus faecalis are hospital-associated opportunistic pathogens and also causative agents of post-operative endophthalmitis. Patients with enterococcal endophthalmitis often have poor visual outcomes, despite appropriate antibiotic therapy. Here we investigated the genomic and phenotypic characteristics of E. faecalis isolates collected from 13 patients treated at the University of Pittsburgh Medical Center Eye Center over 19 years. Comparative genomic analysis indicated that patients were infected with E. faecalis of diverse multi-locus sequence types (STs) previously associated with clinical, commensal, and environmental sources. We identified known E. faecalis virulence factors and antibiotic resistance genes in each genome, including genes conferring resistance to aminoglycosides, erythromycin, and tetracyclines. We assessed all isolates for their cytolysin production, biofilm formation, and antibiotic susceptibility, and observed phenotypic differences between isolates. Fluoroquinolone and cephalosporin susceptibilities were particularly variable, as were biofilm formation and cytolysin production. In addition, we found evidence of E. faecalis adaptation during recurrent endophthalmitis by identifying genetic variants that arose in sequential isolates sampled over eight-months from the same patient. We identified a mutation in the DNA mismatch repair gene mutS that was associated with a hypermutator phenotype in the final isolate from the patient, which was also more resistant to ceftazidime. Overall this study documents the genomic and phenotypic variability among E. faecalis causing endophthalmitis, as well as possible adaptive mechanisms underlying bacterial persistence during recurrent ocular infection.IMPORTANCEBacterial endophthalmitis is a sight-threatening infection of the inside of the eye. Enterococcus faecalis cause endophthalmitis occasionally, but when they do the infections are often severe. Here we investigated the genomes, antibiotic susceptibilities, and virulence-associated traits among E. faecalis collected from 13 patients with post-operative endophthalmitis. We wondered whether there were common bacterial factors that might explain why enterococcal endophthalmitis is so destructive to ocular tissues. Instead we found that E. feacalis isolated from endophthalmitis were genetically and phenotypically diverse; isolates belonged to a variety of genetic lineages and showed varying levels of antibiotic resistance and biofilm formation. We also undertook further characterization of three closely related E. faecalis isolates from a patient with recurrent endophthalmitis, and found that a hypermutator strain emerged during persistent infection. Hypermutators have been found in a variety of other infection contexts; here we describe what we believe is the first case of a hypermutator arising during ocular infection.

show abstract

An extraction‐free method for rapid detection of CYP2C19 * 2/3/17 polymorphisms in one tube using melting curve analysis

Guo

You

Lin

et al. 2023

Biotechnology Journal

View full text Add to dashboard Cite

Drug‐metabolizing enzymes play an important role in the metabolism of drugs in vivo. Their activity is an important factor affecting the rate of drug metabolism, which directly determines the intensity and persistence of drug action. Patients taking medication can be divided into different metabolic types through detection of CYP2C19 drug‐metabolizing enzyme gene polymorphisms, which can then be used for medication guidance for clopidogrel. Here, we describe a detection method based on real‐time polymerase chain reaction. This method uses multicolor melting curve analysis to accurately identify different mutation sites and genotypes of CYP2C19 * 2, CYP2C19 * 3, and CYP2C19 * 17.The detection limit of plasmid samples was 1 copies/μl; that of genomic samples was 0.1 ng/μl. The system can detect nine types of CYP2C19 * 2/3/17 at three sites in one tube, quickly achieving detection within 1 h. Combined with the sample release agent, sample extraction was completed in 5 s, achieving rapid diagnosis without extraction for timely diagnosis and treatment. Furthermore, the system is not limited to blood samples and can also be applied to oropharyngeal and saliva samples, increasing sampling diversity and convenience. When using clinical blood samples (n = 93), the detection system we established was able to quickly and accurately identify different genotypes, and the accuracy and effectiveness of the detection were confirmed by Sanger sequencing.Due to its accuracy, rapidity, simple operation and low cost, detection technology based on real‐time polymerase amplification combined with melting curve analysis is expected to become a powerful tool for detecting and guiding clopidogrel use in countries with limited resources.This article is protected by copyright. All rights reserved

show abstract

Comparative genomics of global optrA-carrying Enterococcus faecalis uncovers a common chromosomal hotspot for optrA acquisition within a diversity of core and accessory genomes

Abstract: Linezolid-resistant Enterococcus faecalis (LREfs) carrying optrA are increasingly reported globally from multiple sources, but we lack a compre… Show more

Cited by 40 publications

References 74 publications

Vigilancia nacional de aislamientos clínicos de Enterococcus faecalis resistentes al linezolid portadores del gen optrA en Colombia, 2014-2019

Vigilancia nacional de aislamientos clínicos de Enterococcus faecalis resistentes al linezolid portadores del gen optrA en Colombia, 2014-2019

Genomic and phenotypic diversity ofEnterococcus faecalisisolated from endophthalmitis

An extraction‐free method for rapid detection of CYP2C19 * 2/3/17 polymorphisms in one tube using melting curve analysis

Contact Info

Product

Resources

About