Antimicrobial Resistance Dynamics in Chilean Shigella sonnei Strains Within Two Decades: Role of Shigella Resistance Locus Pathogenicity Island and Class 1 and Class 2 Integrons.

Shigellosis is an enteric infectious disease in which antibiotic treatment is effective, shortening the duration of symptoms and reducing the excretion of the pathogen into the environment. Shigella spp., the etiologic agent, are considered emerging pathogens with a high public health impact due to the increase and global spread of multidrug-resistant (MDR) strains. Since Shigella resistance phenotype varies worldwide, we present an overview of the resistance phenotypes and associated genetic determinants present in 349 Chilean S. sonnei strains isolated during the periods 1995-1997, 2002-2004, 2008-2009, and 2010-2013. We detected a great variability in antibiotic susceptibility patterns, finding 300 (86%) MDR strains. Mobile genetic elements (MGE), such as plasmids, integrons, and genomic islands, have been associated with the MDR phenotypes. The Shigella resistance locus pathogenicity island (SRL PAI), which encodes for ampicillin, streptomycin, chloramphenicol, and tetracycline resistance genes, was detected by PCR in 100% of the strains isolated in 2008-2009 but was less frequent in isolates from other periods. The presence or absence of SRL PAI was also differentiated by pulsed-field gel electrophoresis. An atypical class 1 integron which harbors the bla OXA-1 -aadA1-IS1 organization was detected as part of SRL PAI. The dfrA14 gene conferring trimethoprim resistance was present in 98.8% of the 2008-2009 isolates, distinguishing them from the SRL-positive strains isolated before that. Thus, it seems an SRL-dfrA14 S. sonnei clone spread during the 2008-2009 period and declined thereafter. Besides these, SRL-negative strains harboring class 2 integrons with or without resistance to nalidixic acid were detected from 2011 onward, suggesting the circulation of another clone. Whole-genome sequencing of selected strains confirmed the results obtained by PCR and phenotypic analysis. It is highlighted that 70.8% of the MDR strains harbored one or more of the MGE evaluated, while 15.2% lacked both SRL PAI and integrons. These results underscore the temporal dynamics of antimicrobial resistance in S. sonnei strains circulating in Chile, mainly determined by the spread of MGE conferring MDR phenotypes. Since shigellosis is endemic in Chile, constant surveillance of antimicrobial resistance phenotypes and their genetic basis is a priority to contribute to public health policies.

[Interactive, semi-automatized and open source computational model applied to respiratory viruses surveillance]. / Modelo computacional interactivo, semi-automatizado y de código abierto aplicado a la vigilancia de virus respiratorios.

Acute respiratory infections (ARI) are an important cause of morbidity and mortality worldwide, affecting mainly children and the elderly. They are associated with a high economic burden, increased number of medical visits and hospitalizations. The surveillance of the circulation of respiratory viruses can reduce the health care associated costs, and to optimize the health response. A platform based on R and its package Shiny was designed, to create an interactive and friendly web interface for gathering, analysis and publication of the data. The data from the Chilean metropolitan respiratory viruses surveillance network, available since 2006, was uploaded into the platform. Using this platform, the researcher spends less than 1 minute to upload the data, and the analysis and publication is immediate, available to be seen by any user with a device connected to Internet, who can choose the variables to be displayed. With a very low cost, in a short time, and using the R programming language, it was possible to create a simple, and interactive platform, considerably decreasing the upload and analysis time, and increasing the impact and availability of this surveillance.

Modelo computacional interactivo, semi-automatizado y de código abierto aplicado a la vigilancia de virus respiratorios / Interactive, semi-automatized and open source computational model applied to respiratory viruses surveillance

Resumen Las infecciones respiratorias agudas (IRA) causadas por virus son una importante causa de morbilidad y mortalidad en el mundo, afectando principalmente a niños y adultos mayores. Se asocian a un alto número de consultas y hospitalizaciones, a una significativa sobrecarga del sistema de salud y a un alto costo económico. La vigilancia de virus respiratorios tiene el potencial de ayudar a optimizar la respuesta sanitaria, garantizar la disponibilidad de recursos humanos, racionalizar los recursos y disminuir los costos asociados a la atención en salud. Con el objetivo de optimizar la recolección y visualización de los datos de nuestro actual sistema de vigilancia de virus respiratorios, se diseñó una plataforma basada en R y sus paquetes Shiny, que permite la creación de una interfase web interactiva y amigable para la recolección, análisis y publicación de los datos. Se ingresaron a esta plataforma los datos de la red de vigilancia metropolitana de virus respiratorios disponibles desde 2006. En esta plataforma, el investigador demora menos de un minuto en registrar los datos. El análisis y publicación es inmediato, llegando a cualquier usuario con un dispositivo conectado a Internet, quien puede elegir las variables a consultar. Con un costo muy bajo, en poco tiempo y utilizando el lenguaje de programación R, se logró crear un sistema simple e interactivo, disminuyendo el tiempo de carga y análisis de datos de forma considerable, posiblemente aumentando el impacto y la disponibilidad de esta vigilancia.

Abstract Acute respiratory infections (ARI) are an important cause of morbidity and mortality worldwide, affecting mainly children and the elderly. They are associated with a high economic burden, increased number of medical visits and hospitalizations. The surveillance of the circulation of respiratory viruses can reduce the health care associated costs, and to optimize the health response. A platform based on R and its package Shiny was designed, to create an interactive and friendly web interface for gathering, analysis and publication of the data. The data from the Chilean metropolitan respiratory viruses surveillance network, available since 2006, was uploaded into the platform. Using this platform, the researcher spends less than 1 minute to upload the data, and the analysis and publication is immediate, available to be seen by any user with a device connected to Internet, who can choose the variables to be displayed. With a very low cost, in a short time, and using the R programming language, it was possible to create a simple, and interactive platform, considerably decreasing the upload and analysis time, and increasing the impact and availability of this surveillance.

Identificación y sensibilidad antifúngica in vitro de Candida spp. de origen vaginal a fluconazol, clotrimazol y nistatina / Identification and in vitro antifungal susceptibility of vaginal Candida spp. isolates to fluconazole, clotrimazole and nystatin

Objetivo. Identificar especie y determinar la sensibilidad in vitro a clotrimazol, fluconazol y nistatina de 145 aislamientos de Candida spp. Material y métodos. Se utilizó un método de microdilución en caldo (M27-A3) para determinar la concentración inhibitoria mínima (CMI) y además las CMI50 y CMI90 de los antifúngicos. De los 145 aislamientos, 126 correspondieron a C. albicans, 16 C. glabrata, 2 C. parapsilosis y 1 C. tropicalis. Resultados. La CMI50 y CMI90 de fluconazol frente C. albicans fueron de 0,25 mg/L y 1 mg/L y para C. glabrata de 8 y 16 mg/L, respectivamente. Cinco aislados de C. albicans y un aislado de C. tropicalis fueron resistentes a fluconazol (M27- S4). Las CIM50 y CIM90 de clotrimazol frente a C. albicans fueron 0,03 mg/L y 0,06 mg/L y para C. glabrata de 0,25 mg/L y 1 mg/L, mientras que para nistatina fueron de 1 mg/L y de 2 mg/L, respectivamente para C. albicans y C. glabrata. Cinco aislados de C. glabrata y 1 de C. tropicalis fueron resistentes a clotrimazol. Conclusión. En este estudio, C. albicans es la levadura más frecuentemente aislada, seguida de C glabrata. Los antifúngicos evaluados resultaron ser activos in vitro para las cepas aisladas, excepto en 6 aislados para fluconazol y 6 para clotrimazol (AU)

Objective. The aim of this study was to identify and determine the in vitro antifungal susceptibility testing to clotrimazole, fluconazole, and nystatin of 145 clinical isolates of Candida spp. Material and methods. M27-A3 microdilution method was used to determine minimal inhibitory concentrations (MIC) and partial MICs (MIC50 and MIC90) of drugs. A total of 145 isolates were studied, 126 were C. albicans, 16 C. glabrata, 2 C. parapsilosis y 1 C. tropicalis. Results. MIC50 and MIC90 for FLZ against C. albicans were 0.25 mg/L and 1 mg/L respectively and for C. glabrata was achieved at 8 mg/L and 16 mg/L for fluconazole. Five isolates of C. albicans and one isolate of C. tropicalis were in vitro resistant to fluconazole (M27-S4). In C. albicans MIC50 and MIC90 for clotrimazole were of 0.03 mg/L and 0.06 mg/L, respectively. These values for C. glabrata were 0.25 mg/L and 1 mg/L, respectively. Five C. glabrata and 1 C. tropicalis were in vitro resistant to clotrimazole. MIC50 and MIC90 of nystatin were of 1 mg/L and 2 mg/L, respectively for C. albicans and C. glabrata. Conclusion. In this study, C. albicans is the most frequently isolated yeast, followed by C glabrata. The antifungals tested were found to be in vitro active for the isolates, except for 6 isolates for fluconazole and 6 to clotrimazole (AU)