Performance of four different diagnostic tests for C. difficile infection in piglets

Clostridium difficile is emerging as a pathogen in man as well as in animals. In 2000 it was described as a cause of neonatal enteritis in piglets and it is now the most common cause of neonatal diarrhoea in the USA. In Europe, C. difficile infection (CDI) in neonatal piglets has also been reported. Diagnosis of this infection is based on detection of the bacterium or its toxins A and B

Syndromic Surveillance for Local Outbreaks of Lower-Respiratory Infections: Would It Work?

Background: Although syndromic surveillance is increasingly used to detect unusual illness, there is a debate whether it is useful for detecting local outbreaks. We evaluated whether syndromic surveillance detects local outbreaks of lower-respiratory infections (LRIs) without swamping true signals by false alarms. Methods and Findings: Using retrospective hospitalization data, we simulated prospective surveillance for LRI-elevations. Between 1999–2006, a total of 290762 LRIs were included by date of hospitalization and patients place of residence (>80% coverage, 16 million population). Two large outbreaks of Legionnaires disease in the Netherlands were used as positive controls to test whether these outbreaks could have been detected as local LRI elevations. We used a space-time permutation scan statistic to detect LRI clusters. We evaluated how many LRI-clusters were detected in 1999–2006 and assessed likely causes for the cluster-signals by looking for significantly higher proportions of specific hospital discharge diagnoses (e.g. Legionnaires disease) and overlap with regional influenza elevations. We also evaluated whether the number of space-time signals can be reduced by restricting the scan statistic in space or time. In 1999–2006 the scan-statistic detected 35 local LRI clusters, representing on average 5 clusters per year. The known Legionnaires' disease outbreaks in 1999 and 2006 were detected as LRI-clusters, since cluster-signals were generated with an increased proportion of Legionnaires disease patients (p:<0.0001). 21 other clusters coincided with local influenza and/or respiratory syncytial virus activity, and 1 cluster appeared to be a data artifact. For 11 clusters no likely cause was defined, some possibly representing as yet undetected LRI-outbreaks. With restrictions on time and spatial windows the scan statistic still detected the Legionnaires' disease outbreaks, without loss of timeliness and with less signals generated in time (up to 42% decline). Conclusions: To our knowledge this is the first study that systematically evaluates the performance of space-time syndromic surveillance with nationwide high coverage data over a longer period. The results show that syndromic surveillance can detect local LRI-outbreaks in a timely manner, independent of laboratory-based outbreak detection. Furthermore, since comparatively few new clusters per year were observed that would prompt investigation, syndromic hospital-surveillance could be a valuable tool for detection of local LRI-outbreaks. (aut. ref.

Mapping spatial distribution and geographic shifts of east African highland banana (Musa spp.) in Uganda

Open Access Journal; Published online: 17 Feb 2022East African highland banana (Musa acuminata genome group AAA-EA; hereafter referred to as banana) is critical for Uganda’s food supply, hence our aim to map current distribution and to understand changes in banana production areas over the past five decades. We collected banana presence/absence data through an online survey based on high-resolution satellite images and coupled this data with independent covariates as inputs for ensemble machine learning prediction of current banana distribution. We assessed geographic shifts of production areas using spatially explicit differences between the 1958 and 2016 banana distribution maps. The biophysical factors associated with banana spatial distribution and geographic shift were determined using a logistic regression model and classification and regression tree, respectively. Ensemble models were superior (AUC = 0.895; 0.907) compared to their constituent algorithms trained with 12 and 17 covariates, respectively: random forests (AUC = 0.883; 0.901), gradient boosting machines (AUC = 0.878; 0.903), and neural networks (AUC = 0.870; 0.890). The logistic regression model (AUC = 0.879) performance was similar to that for the ensemble model and its constituent algorithms. In 2016, banana cultivation was concentrated in the western (44%) and central (36%) regions, while only a small proportion was in the eastern (18%) and northern (2%) regions. About 60% of increased cultivation since 1958 was in the western region; 50% of decreased cultivation in the eastern region; and 44% of continued cultivation in the central region. Soil organic carbon, soil pH, annual precipitation, slope gradient, bulk density and blue reflectance were associated with increased banana cultivation while precipitation seasonality and mean annual temperature were associated with decreased banana cultivation over the past 50 years. The maps of spatial distribution and geographic shift of banana can support targeting of context-specific intensification options and policy advocacy to avert agriculture driven environmental degradation