ABTRACT Introduction: Recent efforts in the diagnosis of SARS-CoV-2 have focused on the development of rapid tests for the detection of SARS-CoV-2 antigens (RTD-Ag), due to the low cost of these methods and the speed to provide a primary diagnosis at the point of care outside the laboratory. In this study, the utility of five methods for detecting the nucleocapsid protein (N) of SARS-CoV-2 as an antigen (Ag) for the positive diagnosis of this virus was evaluated. Methods: Five kits for the detection of SARS-CoV-2 Ag based on two molecular principles (immunochromatography and immunofluorescence) were evaluated. A total of 587 samples from nasal and nasopharyngeal swab of patients confirmed by RT-PCR to SARS-CoV-2 and negative samples to this virus were analyzed. Sensitivity, specificity, Positive Predictive Value (PPV), Negative Predictive Value (NPV), concordance and Kappa index parameters were calculated for each assay evaluated. Results: The ABBOTT, CPM, CORE and WANTAI SARS-CoV-2 (IFA) assays performed well (sensitivity: 80-95 % and specificity 90-98 %) when evaluated with samples from suspected patients. In the KEWEI trial, the results of these parameters differed (75 % sensitivity and 90 % specificity) from those recommended by the WHO. According to the Kappa index rating scale, all the trials analyzed showed good and very good agreement. Conclusions: The results obtained in this research support the utility of the tests evaluated and their use in the network of laboratories for the diagnosis of SARS-CoV-2.

RESUMEN Introducción: Los esfuerzos recientes en el diagnóstico del SARS-CoV-2 se han centrado en el desarrollo de pruebas rápidas de detección de antígenos SARS-CoV-2 (PRD-Ag), debido al bajo costo de estos métodos y a la rapidez para brindar un diagnóstico primario en el punto de atención médica fuera del laboratorio. En este estudio se evaluó la utilidad de cinco métodos de detección de la proteína de la nucleocápside (N) del SARS-CoV-2 como antígeno (Ag) para el diagnóstico de este virus. Métodos: Se evaluaron cinco estuches para la detección de Ag SARS-CoV-2 basados en dos principios moleculares (inmunocromatografía e inmunofluorescencia). Se analizó un total de 587 muestras procedentes de exudado nasal y nasofaríngeo de pacientes confirmados por la Reacción en Cadena de la Polimerasa en Tiempo Real (RT-PCR) al SARS-CoV-2 y muestras negativas a este virus. Se calcularon los parámetros de sensibilidad, especificidad, Valor Predictivo Positivo (VPP), Valor Predictivo Negativo (VPN), concordancia e índice Kappa para cada ensayo evaluado. Resultados: Los ensayos ABBOTT, CPM, CORE y WANTAI SARS-CoV-2 (IFA) presentaron un buen desempeño (sensibilidad: 80-95 % y especificidad 90-98 %) al ser evaluados con muestras de pacientes sospechosos. En el ensayo KEWEI los resultados de estos parámetros difirieron (sensibilidad del 75 % y especificidad del 90 %) de los recomendados por la OMS. Según la escala de valoración del índice de Kappa, todos los ensayos analizados presentaron un grado de concordancia Buena y Muy buena. Conclusiones: Los resultados obtenidos en la presente investigación, avalan la utilidad de los ensayos evaluados y su uso en la red de laboratorios para el diagnóstico del SARS-CoV-2.

Abstract INTRODUCTION Urinary tract infection is the second-leading reason for consults in primary health care. Bacterial urinary tract infections are the most common, of which Escherichia coli is the main etiologic agent. Antimicrobial resistance and multidrug resistance complicate effective community treatment, especially if resistance is caused by extended-spectrum beta-lactamase production. WHO recommends that antimicrobial susceptibility be evaluated in different regions of the world at different times. Community-acquired E. coli’s susceptibility to colistin has not yet been studied in Cuba, and mcr-1 gene screening is necessary. OBJECTIVE Evaluate community-acquired uropathogenic E. coli isolates’ susceptibility to antibiotics, including colistin, and identify extended-spectrum beta-lactamase–producing bacteria. METHODS We conducted a descriptive cross-sectional study that included 281 community-acquired uropathogenic E. coli isolates (153 from the Isle of Youth Special Municipality’s Hygiene, Epidemiology, and Microbiology Center and 128 from Microbiology Laboratories of 7 institutions in Havana) from June 2016 through July 2018. We used the disk diffusion method to determine susceptibility to ampicillin, ampicillin/sulbactam, cefazolin, trimethoprim/sulfamethoxazole, ciprofloxacin, nitrofurantoin and fosfomycin. The disk elution method was used to determine susceptibility to colistin. The combined disk method was used to identify extended-spectrum beta-lactamases. Estimates were made regarding the frequency and percentages of antimicrobial susceptibility and resistance, as well as multidrug-resistance patterns. RESULTS Of the 281 isolates, 68.3% (192/281) were resistant to ampicillin, 54.8% (154/281) were resistant to ciprofloxacin, and 49.5% (139/281) were resistant to trimethoprim/sulfamethoxazole. Resistance to colistin was not detected. On the other hand, 14.2% (40/281) were susceptible to the 8 antibiotics we evaluated, 22.1% (62/281) showed resistance to only 1 antibiotic, and 63.7% (179/281) were resistant to 2 or more antibiotics. In the extended-spectrum beta-lactamase determination, 34.5% (97/281) had inhibition zones ≤14 mm with cefazolin. Of those with inhibition zones, 64.9% (63/97) were positive in the phenotype test, and 35.1% (34/97) were negative. In extended-spectrum beta-lactamase–producing bacteria, 1.6% (1/63) were resistant to fosfomycin, and 3.2% (2/63) were resistant to nitrofurantoin. The most common multidrug-resistance pattern (22.9%; 30/131) was to ampicillin/sulbactam, ampicillin, cefazolin, ciprofloxacin, and trimethoprim/sulfamethoxazole. CONCLUSIONS Uropathogenic E. coli resistance to the antibiotics most frequently used in community medical practice is quite common, and extended-spectrum beta-lactamase–producing bacteria is the mechanism for beta-lactam antibiotic resistance. Multidrug-resistance patterns include resistance to the antibiotics most used in community-acquired infections. Fosfomycin and nitrofurantoin are the most active in extended-spectrum beta-lactamase producing bacteria. All the isolates were susceptible to colistin.

ABSTRACT Introduction: Extraintestinal Escherichia coli is one of the main pathogens causing infections associated to health care, with a high impact on health, due to its morbidity and mortality. Objective: Describe the clinical behavior of extraintestinal E. coli in Cuban hospitals, and determine antimicrobial resistance and betalactamase production. Methods: A descriptive cross-sectional study was conducted at the Microbiology National Reference Laboratory of Pedro Kourí Tropical Medicine Institute from May 2017 to June 2018. The study included 119 Escherichia coli isolates causing extraintestinal infections in 30 hospitals from various geographic areas in the country. Identification was based on the API 20E system, and determination of in vitro susceptibility to 16 antimicrobials on the automated system VITEK-2 and the disk diffusion method, except for colistin, for which the disk elution method was used. Phenotypical detection was also performed of AmpC extended-spectrum betalactamase and metallobetalactamase. Results: The most common disorders caused by extraintestinal E. coli were surgical wound infection (23.5%), bloodstream infection (20.7%), respiratory infections (17.6%), skin infections (16.8%) and urinary tract infection (12.6%). A predominance was found of resistance to betalactams, which ranged between 61.3% y 89.1%, whereas 79.8% and 80.5% of the isolates were resistant to trimethoprim / sulfamethoxazole and tetracycline, respectively. Amikacin, fosfomycin, colistin and carbapenemics displayed greater in vitro activity. 43.7% produced extended spectrum betalactamases, 7.6% plasmid AmpC and 0.8% metallobetalactamase. Conclusions: The low sensitivity of extraintestinal E. coli isolates to first-line antimicrobials and the detection of a metallobetalactamase producing isolate are evidence of the need to maintain continuous surveillance of this pathogen, for which the treatment options are ever more restricted.

RESUMEN Introducción: Escherichia coli extraintestinal constituye uno de los principales patógenos causantes de infecciones asociadas a la asistencia sanitaria con un alto impacto en la salud por su morbilidad y mortalidad. Objetivo: Describir el comportamiento clínico de E. coli extraintestinal en hospitales cubanos, así como determinar la resistencia antimicrobiana y la producción de betalactamasas. Métodos: Se realizó un estudio descriptivo de corte transversal, durante el período de mayo 2017 a junio 2018, en el Laboratorio Nacional de Referencia de Microbiología del Instituto de Medicina Tropical “Pedro Kourí" que incluyó 119 aislados de Escherichia coli causantes de infecciones extraintestinales en 30 hospitales de diferentes áreas geográficas del país. Se llevó a cabo la identificación mediante el sistema API 20E y la determinación de la susceptibilidad in vitro a 16 antimicrobianos por el sistema automatizado VITEK-2 y el método de difusión por disco, excepto para la colistina que se empleó el método de elución de disco. Se realizó, además, la detección fenotípica de betalactamasa de espectro extendido, de tipo AmpC y metalobetalactamasa. Resultados: E. coli extraintestinal causó con mayor frecuencia infección de herida quirúrgica (23,5 %), infección del torrente sanguíneo (20,7 %), infecciones respiratorias (17,6 %), infecciones de piel (16,8 %) e infección del tracto urinario (12,6 %). Predominó la resistencia a betalactámicos que osciló entre 61,3 % y 89,1 %, mientras que 79,8 % y 80,5 % de los aislados fueron resistentes a trimetoprim/sulfametoxazol y tetraciclina, respectivamente. La amikacina, la fosfomicina, la colistina y los carbapenémicos mostraron mayor actividad in vitro. El 43,7 % produjo betalactamasas de espectro extendido, 7,6 % AmpC plasmídica y 0,8 % metalobetalactamasa. Conclusiones: La escasa sensibilidad en los aislados de E. coli extraintestinal a los antimicrobianos de primera línea, así como la detección de un aislado productor de metalobetalactamasa evidencia la necesidad de mantener un monitoreo continuo de este patógeno para el cual las alternativas de tratamiento son cada vez más restringidas.