Association between lockdown and changes in subspecies diversity with a focus on Haemophilus influenzae and Staphylococcus aureus

BackgroundThe social distancing measures implemented to curb SARS-CoV-2 transmission provided a unique opportunity to study the association between reduced human interaction and epidemiological changes related to human bacterial pathogens. While studies have indicated a decrease in respiratory infections during lockdowns, further description is needed regarding the changes in the incidence of bacterial populations. This study investigates the changes in strain richness of community infections with two bacterial species, Haemophilus influenzae and Staphylococcus aureus during the waning related to Frances social distancing measures, especially lockdown. MethodsMALDI-TOF MS spectra analyses of routine clinical bacterial identifications were used as proxies for genomic analyses. Spectra from lockdown and reference periods were compared using unsupervised classification methods. A total of 251 main spectrum profiles of H. influenzae, 2079 main spectrum profiles of S. aureus for respiratory tract and blood samples, and 414 main spectrum profiles for skin samples of S. aureus were examined. Data were analyzed using hierarchical clustering, binary discriminant analysis, and statistical tests for significance. ResultsThe strain mix of both bacteria during the lockdown was deeply altered, but with different further evolutions. H. influenzae exhibited a shift in spectra composition, with a subsequent return towards pre-lockdown diversity observed in 2021. In contrast, S. aureus exhibited a persistent change in spectra composition, with a gradual return to pre-lockdown patterns one year later. ConclusionsHindering inter-human transmission, as was done during the lockdown measures, was associated with significant alterations in bacterial species compositions, with differential impacts observed for H. influenzae and S. aureus. This study provides data on the putative relationship between genetic diversity and transmission dynamics during a public health crisis. Describing the dynamics of bacterial populations during lockdowns could contribute providing information for the implementation of future strategies for infectious disease control and surveillance.