Evaluation of reverse transcription-loop-mediated isothermal amplification for rapid detection of SARS-CoV-2.

The main strategy for response and control of COVID-19 demands the use of rapid, accurate diagnostic tests aimed at the first point of health care. During the emergency, an increase in asymptomatic and symptomatic cases results in a great demand for molecular tests, which is promoting the development and application of rapid diagnostic technologies. In this study, we describe the development and evaluation of RT-LAMP to detect SARS-CoV-2 based on three genes (ORF1ab, M and N genes) in monoplex and triplex format. RT-LAMP assays were compared with the gold standard method RT-qPCR. The triplex format (RdRp, M and N genes) allowed obtaining comparable results with de RT-qPCR (RdRp and E genes), presented a sensitivity of 98.9% and a specificity of 97.9%, opening the opportunity to apply this method to detect SARS-CoV-2 at primary health-care centers.

Phylogenetic structure of Salmonella Enteritidis provides context for a foodborne outbreak in Peru.

Salmonella Enteritidis, an important foodborne zoonosis, has a dramatically increased number of cases around the world. To explore the phylogenetic structure of Peruvian Salmonella Enteritidis strains and their relationship with an outbreak occurred in 2018, we analyzed a comprehensive strains of S. Enteritidis received by the National Institute of Health during the period 2000-2018. A total of 180 strains were characterized by microbiological procedures, serotyping and whole genome sequencing. Based on genome sequences annotated, virulence factors and accessory genes were identified. Phylogenetic and population structure analysis were also analyzed based on SNPs. The phylogenetic analysis grouped the genomes into two well-supported clades that were consistent with population structure analysis. The clinical and food strains corresponding to the outbreak were included in the same cluster, which presented the sdhA gene, related to the increase of the virulence of this pathogen. The phylogenetic relationship of Peruvian S. Enteritidis suggests the presence of four S. enteritidis population with high epidemiological importance.

Patrones de resistencia a los antimicrobianos en serovares de Salmonella enterica en Perú, 2012-2015 / Patterns of resistance to antimicrobials in serovars of Salmonella enterica in Peru, 2012-2015

Resumen Introducción: La salmonelosis es una zoonosis universal, causante de frecuentes brotes de enfermedades transmitidas por alimentos; Salmonella enterica es la especie con la mayor prevalencia, describiéndose un aumento progresivo de su resistencia a antimicrobianos. Objetivo: Determinar la frecuencia de serotipos y los patrones de resistencia antimicrobiana en aislados de S. enterica remitidos al Instituto Nacional de Salud, Lima, Perú. Materiales y Métodos: Se realizó un estudio descriptivo, transversal. Se incluyeron en el estudio todas las cepas remitidas como parte de la vigilancia nacional basada en laboratorio entre los años 2012 y 2015. Las cepas fueron confirmadas mediante pruebas convencionales y serotipificadas por el esquema de Kauffmann-White; la susceptibilidad antimicrobiana y la confirmación del fenotipo BLEE se realizó según el método de Kirby-Bauer y método de Jarlier. Resultados: Un total de 540 cepas de S. enterica fueron incluidos en el estudio, de las que 96% (520/540) correspondió a cepas de origen humano y 4% (20/540) de origen no humano (aves, alimentos y ambiental). En muestras humanas, el serovar más frecuente fue S. Infantis (57%), seguido de S. Enteritidis (27%) y S. Typhimurium (6%). Se encontró una alta resistencia a nitrofurantoína (74%), ácido nalidíxico (64%), ciprofloxacina (63%), tetraciclina (63%), ampicilina (56%), cotrimoxazol (56%), cefotaxima (53%) y cloranfenicol (50%). En muestras no humanas, el serotipo más frecuente fue S. Infantis (45%), seguido de S. Typhimurium (40%) y S. Enteritidis (10%). encontrándose una alta resistencia a ciprofloxacina (45%), cotrimoxazol (40%), y tetraciclina (40%). El 65% del total de las cepas presentó resistencia a más de dos antimicrobianos, 43,3% fueron productoras de BLEE y 99% de éstas presentaron resistencia a entre seis y ocho antimicrobianos. Conclusiones: Se encontró una alta frecuencia de Salmonella Infantis productoras de BLEE, con multi-resistencia a los antimicrobianos en los aislados de muestras humanas y no humanas recibidas en el Instituto Nacional de Salud.

Abstract Background: Salmonellosis is a universal zoonosis, causing frequent outbreaks of foodborne illness; Salmonella enterica is the species with the highest prevalence, a progressive increase in its resistance to antimicrobials is described. Aim: To determine the frequency of serovars and antimicrobial resistance patterns in S. enterica isolates submitted to the National Institute of Health, Lima, Peru. Methods: This is a cross-sectional study. All strains referred as part of national laboratory-based surveillance between 2012 and 2015 were included in the study. Strains were confirmed by conventional tests and serotyped by the Kauffmann-White scheme; antimicrobial susceptibility and confirmation of the BLEE phenotype was performed according to the method of Kirby-Bauer and Jarlier's method. Results: A total of 540 strains of S. enterica were included in the study, where 96% (520/540) corresponded to human strains and 4% (20/540) to non-human strains (birds, food and environmental). In human samples, the most frequent serovar was S. Infantis (57%), followed by S. Enteritidis (27%) and S. Typhimurium (6%). High resistance to nitrofurantoin (74%), nalidixic acid (64%), ciprofloxacin (63%), tetracycline (63%), ampicillin (56%), sulfamethoxazole-trimethoprim (56%), cefotaxime (53%) and chloramphenicol (50%) was detected. In non-human samples, the most frequent serotype was S. Infantis (45%), followed by S. Typhimurium (40%) and S. Enteritidis (10%); a high resistance to nalidixic acid (55%), ciprofloxacin (45%), sulfamethoxazole-trimethoprim (40%), nitrofurantoin (40%), tetracycline (40%) was found. 65% of all strains had resistance to more than two antibiotics, 43,3% were ESBL producers and 99% of these had resistance between six and eight antibiotics. Conclusions: We found a high frequency of S. Infantis producing ESBL with multi-resistance to the antimicrobials in human and nonhuman samples received by the National Institute of Health.

[Patterns of resistance to antimicrobials in serovars of Salmonella enterica in Peru, 2012-2015]. / Patrones de resistencia a los antimicrobianos en serovares de Salmonella enterica en Perú, 2012-2015.

BACKGROUND: Salmonellosis is a universal zoonosis, causing frequent outbreaks of foodborne illness; Salmonella enterica is the species with the highest prevalence, a progressive increase in its resistance to antimicrobials is described. AIM: To determine the frequency of serovars and antimicrobial resistance patterns in S. enterica isolates submitted to the National Institute of Health, Lima, Peru. METHODS: This is a cross-sectional study. All strains referred as part of national laboratory-based surveillance between 2012 and 2015 were included in the study. Strains were confirmed by conventional tests and serotyped by the Kauffmann-White scheme; antimicrobial susceptibility and confirmation of the BLEE phenotype was performed according to the method of Kirby-Bauer and Jarlier's method. RESULTS: A total of 540 strains of S. enterica were included in the study, where 96% (520/540) corresponded to human strains and 4% (20/540) to non-human strains (birds, food and environmental). In human samples, the most frequent serovar was S. Infantis (57%), followed by S. Enteritidis (27%) and S. Typhimurium (6%). High resistance to nitrofurantoin (74%), nalidixic acid (64%), ciprofloxacin (63%), tetracycline (63%), ampicillin (56%), sulfamethoxazole-trimethoprim (56%), cefotaxime (53%) and chloramphenicol (50%) was detected. In non-human samples, the most frequent serotype was S. Infantis (45%), followed by S. Typhimurium (40%) and S. Enteritidis (10%); a high resistance to nalidixic acid (55%), ciprofloxacin (45%), sulfamethoxazole-trimethoprim (40%), nitrofurantoin (40%), tetracycline (40%) was found. 65% of all strains had resistance to more than two antibiotics, 43,3% were ESBL producers and 99% of these had resistance between six and eight antibiotics. CONCLUSIONS: We found a high frequency of S. Infantis producing ESBL with multi-resistance to the antimicrobials in human and nonhuman samples received by the National Institute of Health.