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

Cherrie, Mark P. C.; Nichols, Gordon; Iacono, Gianni Lo; Sarran, Christophe; Hajat, Shakoor; Fleming, Lora E.

The weekly data on 12.9 million pathogen infections in England and Wales from 1989 to 2014 were examined systematically. The minimum number for an organism to be in the database during the time period was once per week. The maximum number of cases for 1 week was 4073 for Chlamydia trachomatis. There was a non-normal distribution of total cases, from one case for 345 organisms to 2,094,656 for Chlamydia trachomatis. The median number of total cases was 3156 (Interquartile range quartile 1-quartile 3; 854-15,730). The organisms with the highest number of serotypes were Salmonella (n = 890) and Streptococcus (n = 60), although most of these had very low counts. Figure 1 shows a heat map of z-scores of crude rates by month ( Fig. 1 shows non-salmonella pathogens, and Fig. 1 shows only the Salmonella genus). The months with the fewest high pathogen rates for the majority of organisms were December (36.1%) and February (31.4%). The months with the highest number of high pathogen rates were more evenly spread out over the summer and autumn, with July, August, September and October being the highest months for 62.2% of the organisms. The seasonality of gastro-intestinally acquired infections (Fig. 2) , and pathogens acquired through respiratory transmission (Fig. 3) , differed substantially. The gastro-intestinal pathogens showed different distributions, with most bacteria having higher rates in summer, some viruses had higher rates in winter (e.g. norovirus, rotavirus) and others were more common in the summer (enteroviruses). Some of the pathogens associated with travel overseas had a late summer increase (thought to reflect the period when people return from summer holidays). The respiratory pathogens predominated in the winter months (e.g. coronavirus, influenza, Respiratory Syncytial Virus (RSV)). However, several of the bacterial pathogens were more frequent in warmer months (e.g. Bordetella, Coxiella, Legionella).