Near real-time surveillance of the SARS-CoV-2 epidemic with incomplete data

When responding to infectious disease outbreaks, rapid and accurate estimation of the epidemic trajectory is critical. However, two common data collection problems affect the reliability of the epidemiological data in real time: missing information on the time of first symptoms, and retrospective revision of historical information, including right censoring. Here, we propose an approach to construct epidemic curves in near real time that addresses these two challenges by 1) imputation of dates of symptom onset for reported cases using a dynamically-estimated "backward" reporting delay conditional distribution, and 2) adjustment for right censoring using the NobBS software package to nowcast cases by date of symptom onset. This process allows us to obtain an approximation of the time-varying reproduction number (Rt) in real time. We apply this approach to characterize the early SARS-CoV-2 outbreak in two Spanish regions between March and April 2020. We evaluate how these real-time estimates compare with more complete epidemiological data that became available later. We explore the impact of the different assumptions on the estimates, and compare our estimates with those obtained from commonly used surveillance approaches. Our framework can help improve accuracy, quantify uncertainty, and evaluate frequently unstated assumptions when recovering the epidemic curves from limited data obtained from public health systems in other locations.PMD was supported by the fellowship Ramón Areces Foundation. JAH was funded by the National Institute of General Medical Sciences, Award U54GM088558, and the National Institutes of Health Director’s Early Independence, Award DP5-OD028145. ML was supported by the Morris-Singer Fund and by a subcontract from the Carnegie Mellon University under an award from the US Centers for Disease Control and Prevention, Award U01IP001121). MS was supported by the National Institute Of General Medical Sciences, Award R01GM130668-02. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.S

Emergence of KPC-producing Klebsiella pneumoniae in Uruguay: infection control and molecular characterization

We describe the first outbreak of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae (KPC-KP), the infection control measures adopted and the shift in resistance patterns of isolates during antibiotic treatment. The ST258 KPC-KP strain exhibited a multiresistant antibiotic phenotype including co-resistance to gentamycin, colistin and tigecycline intermediate susceptibility. Isolates before and after treatment had different behaviour concerning their antibiotic susceptibility and the population analysis profile study. A progressive increase in the aminoglycosides (acquiring amicacin resistance) and β-lactam MICs, and a decreased susceptibility to fosfomycin was observed throughout the administration of combined antimicrobial regimens including meropenem. A high meropenem resistance KPC-KP homogeneous population (MIC 256 Jg/mL), could arise from the meropenem heterogeneous low-level resistance KPC-KP population (MIC 8 Jg/mL), by the selective pressure of the prolonged meropenem therapy. The kpc gene was inserted in a Tn4401 isoform a, and no transconjugants were detected. The core measures adopted were successful to prevent evolution towards resistance dissemination

Metodología y logística de campo de un estudio multinivel sobre la influencia en España de las características medioambientales en la salud mental de población autóctona y ecuatoriana inmigrante

Se realizó una investigación multinivel sobre el impacto de las características ambientales de la zona de residencia en la salud mental de población autóctona e inmigrante. El objetivo de este artículo es describir el planteamiento metodológico de la investigación, el trabajo de campo, las tasas de respuesta correspondientes y discutir el diseño metodológico y las dificultades derivadas de su puesta en práctica. Los datos individuales se obtuvieron aplicando un cuestionario estructurado de aproximadamente 40 minutos, mediante entrevista domiciliaria a personas españolas y ecuatorianas de 18 a 55 años. El trabajo se realizó de septiembre de 2006 a enero de 2007 en una muestra estimada de 1.186 personas equiparada por sexo y nacionalidad, obtenida aleatoriamente de los Padrones Municipales de 33 áreas (municipios o barrios) de Madrid, Alicante, Almería y Murcia, seleccionadas según criterios de densidad étnica y socioeconómicos. Previamente se realizó un estudio piloto (n=113)Los indicadores sociodemográficos de las áreas se obtuvieron a partir de fuentes secundarias. Se entrevistó a 1.144 personas (96%). La tasa de respuesta global fue del 61%, superior entre ecuatorianos (69%), colectivo que presentó más problemas de localización (34%). Las negativas a colaborar fueron más altas entre españoles (21%). Se concluye que en este tipo de estudios sería conveniente revisar las estrategias de muestreo para combinar criterios de eficiencia con la necesidad de obtener una muestra representativa de la población diana. Se constata la dificultad de obtener datos inframunicipales de integración social

Population structure of Environmental and Clinical Legionella pneumophila isolates in Catalonia

Abstract Legionella is the causative agent of Legionnaires’ disease (LD). In Spain, Catalonia is the region with the highest incidence of LD cases. The characterisation of clinical and environmental isolates using molecular epidemiology techniques provides epidemiological data for a specific geographic region and makes it possible to carry out phylogenetic and population-based analyses. The aim of this study was to describe and compare environmental and clinical isolates of Legionella pneumophila in Catalonia using sequence-based typing and monoclonal antibody subgrouping. A total of 528 isolates were characterised. For data analysis, the isolates were filtered to reduce redundancies, and 266 isolates (109 clinical and 157 environmental) were finally included. Thirty-two per cent of the clinical isolates were ST23, ST37 and ST1 while 40% of the environmental isolates were ST284 and ST1. Although the index of diversity was higher in clinical than in environmental ST isolates, we observed that clinical STs were similar to those recorded in other regions but that environmental STs were more confined to particular study areas. This observation supports the idea that only certain STs trigger cases or outbreaks in humans. Therefore, comparison of the genomes of clinical and environmental isolates could provide important information about the traits that favour infection or environmental persistence