Pathogen seasonality and links with weather in England and Wales: a big data time series analysis

BMC Public Health
Mark P C CherrieLora E Fleming

Abstract

Many infectious diseases of public health importance display annual seasonal patterns in their incidence. We aimed to systematically document the seasonality of several human infectious disease pathogens in England and Wales, highlighting those organisms that appear weather-sensitive and therefore may be influenced by climate change in the future. Data on infections in England and Wales from 1989 to 2014 were extracted from the Public Health England (PHE) SGSS surveillance database. We conducted a weekly, monthly and quarterly time series analysis of 277 pathogen serotypes. Each organism's time series was forecasted using the TBATS package in R, with seasonality detected using model fit statistics. Meteorological data hosted on the MEDMI Platform were extracted at a monthly resolution for 2001-2011. The organisms were then clustered by K-means into two groups based on cross correlation coefficients with the weather variables. Examination of 12.9 million infection episodes found seasonal components in 91/277 (33%) organism serotypes. Salmonella showed seasonal and non-seasonal serotypes. These results were visualised in an online Rshiny application. Seasonal organisms were then clustered into two groups based on their correlatio...Continue Reading

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Citations

Apr 22, 2020·Nature Immunology·Jan C Semenza
Mar 21, 2020·International Journal of Environmental Research and Public Health·Paolo LauriolaGiovanni S Leonardi
Aug 23, 2020·International Journal of Environmental Research and Public Health·Tania M Alarcon FalconiElena N Naumova
Nov 18, 2020·Insects·Marcos Venícius Malveira de Lima, Gabriel Zorello Laporta
Feb 9, 2019·Water Research·Sharon P NappierSorina E Eftim
Jul 16, 2019·Ecotoxicology and Environmental Safety·Mohamad Sakizadeh
Oct 20, 2021·The Lancet Regional Health. Europe·Jan C Semenza, Shlomit Paz

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Software Mentioned

Rstudio
ACINETOBACTER
Rshiny
ArcMap
TBATS
MEDMI Platform
Medical and Environmental Data Mash - up Infrastructure projec...

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