Impact of COVID-19 on sputum isolates and hospital outcomes among patients with pneumonia in Sheffield, United Kingdom: a retrospective cohort study

Background and aim The COVID-19 pandemic caused by SARS-CoV-2 severely affected healthcare globally. Strong links have been suggested between the pandemic and changes in the epidemiology of organisms responsible for non-COVID-19 pneumonia. In this study, we examined temporal changes in organisms recovered from sputum culture, integrating laboratory data from all submitted sputum specimens with clinical data from a subset of patients diagnosed with community-acquired pneumonia (CAP). Method A retrospective study was conducted from August 2017 to May 2024 using data derived from samples from healthcare centres in Sheffield including hospitals, general practices, hospices and other palliative care settings. August 2017 to March 2020, April 2020 to September 2022, and October 2022 to May 2024 were defined as before, during, and after COVID-19 periods, respectively. Absolute percentage-point change in the distribution of organisms was performed at genera level. Results A total of 50,827 culture positive isolate episodes from sputum samples were analysed during the study period, of which 25,085 (45.4%; 783.9 isolate episodes per month), 11,644 (22.9%; 388.1 isolate episodes per month) and 14,098 (27.7%; 704.9 isolate episodes per month) were obtained before, during and after COVID-19, respectively. Overall, the commonest cultured genus were Haemophilus sp. (21,229/50,827, 41.8%), Pseudomonas sp. (5,504/50827, 10.8%), and Streptococcus sp. (4,893/50,827, 9.6%). Haemophilus sp. remained the commonest cultured genus in each period of the study. Streptococcus sp. was the second commonest (2,769/25,085, 11.0%) before COVID-19; fourth commonest (862/11,644, 7.4%) after Pseudomonas sp. (1,672/11,644, 14.4%) and Staphylococcus sp. (1,279/11,644, 11.0%) during COVID-19; and third commonest cultured genus (1,262/14098, 9.0%) after Moraxella sp. (1,360/14,098, 9.6%) during the post-pandemic period. There were significant variations in the proportion of isolates with Haemophilus sp. (−7.9%, p < 0.001) and Pseudomonas sp. (+4.3%, p < 0.001) showing the highest change during COVID-19 compared to prior. Conclusion We found substantial differences in the number of isolate episodes identified. This could present important considerations for treatment of patients presenting with CAP during future pandemics.